[inst/scripts/test_load_data.R:3:27:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L3) *style:* **Put spaces around all infix operators.**
```r
cdata <- data.frame(sample=c("riboz", "RNaseR"),
                         ~^~
```
[inst/scripts/test_load_data.R:4:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L4) *style:* **lines should not be more than 80 characters.**
```r
                    filename=c("inst/extdata/ciri_demo_hek/HEK_riborezo_CIRI_sites.txt",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:4:29:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L4) *style:* **Put spaces around all infix operators.**
```r
                    filename=c("inst/extdata/ciri_demo_hek/HEK_riborezo_CIRI_sites.txt",
                           ~^~
```
[inst/scripts/test_load_data.R:5:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L5) *style:* **lines should not be more than 80 characters.**
```r
                               "inst/extdata/ciri_demo_hek/HEK_RNaseR_CIRI_sites.txt"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:7:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L7) *style:* **Commented code should be removed.**
```r
# colData <- cdata
  ^~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:8:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L8) *style:* **Commented code should be removed.**
```r
# keep.linear <- TRUE
  ^~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:9:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L9) *style:* **Commented code should be removed.**
```r
# wobble <- 1
  ^~~~~~~~~~~
```
[inst/scripts/test_load_data.R:10:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L10) *style:* **Commented code should be removed.**
```r
# subs <- "all"
  ^~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:11:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L11) *style:* **Commented code should be removed.**
```r
# qualfilter <- FALSE
  ^~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:12:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L12) *style:* **Commented code should be removed.**
```r
# keepCols <- 1:12
  ^~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:15:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L15) *style:* **lines should not be more than 80 characters.**
```r
circs.se <- summarizeCircs(colData = cdata, keep.linear = FALSE, wobble = 1, subs = "all", qualfilter = FALSE, keepCols = 1:12)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:16:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L16) *style:* **lines should not be more than 80 characters.**
```r
circs.se <-  annotateCircs(se = circs.se, annot.list = annot.list, assembly = "hg19")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:21:27:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L21) *style:* **Put spaces around all infix operators.**
```r
cdata <- data.frame(sample=c("D0", "D2", "D4"),
                         ~^~
```
[inst/scripts/test_load_data.R:22:29:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L22) *style:* **Put spaces around all infix operators.**
```r
                    filename=c("inst/extdata/Sy5y_D0_sites.bed",
                           ~^~
```
[inst/scripts/test_load_data.R:23:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L23) *style:* **lines should not be more than 80 characters.**
```r
                               "/data/circrna/Human/Sy5y_diff/D2/Sy5y_D2_sites.bed",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:23:33:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L23) *warning:* **Do not use absolute paths.**
```r
                               "/data/circrna/Human/Sy5y_diff/D2/Sy5y_D2_sites.bed",
                                ^~~~~
```
[inst/scripts/test_load_data.R:24:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L24) *style:* **lines should not be more than 80 characters.**
```r
                               "/data/circrna/Human/Sy5y_diff/D4/Sy5y_D4_sites.bed"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:24:33:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L24) *warning:* **Do not use absolute paths.**
```r
                               "/data/circrna/Human/Sy5y_diff/D4/Sy5y_D4_sites.bed"))
                                ^~~~~
```
[inst/scripts/test_load_data.R:28:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L28) *style:* **lines should not be more than 80 characters.**
```r
circs.se <- annotateCircs(se = circs.se, annot.list = annot.list, assembly = "hg19", fixCoordIndexing = T)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:37:2:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L37) *style:* **Commented code should be removed.**
```r
#library(data.table)
 ^~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:38:2:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L38) *style:* **Commented code should be removed.**
```r
#library(GenomicRanges)
 ^~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:39:2:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L39) *style:* **Commented code should be removed.**
```r
#library(hash)
 ^~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:40:2:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L40) *style:* **Commented code should be removed.**
```r
#annot.list <- loadAnnotation("data/test.sqlite")
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:42:27:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L42) *style:* **Put spaces around all infix operators.**
```r
cdata <- data.frame(sample=c("FC1", "FC2", "H1", "H2", "L1", "L2"),
                         ~^~
```
[inst/scripts/test_load_data.R:43:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L43) *style:* **lines should not be more than 80 characters.**
```r
                    filename=dir("inst/extdata/", full.names=T)[grep("rep", dir("inst/extdata/"))])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:43:29:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L43) *style:* **Put spaces around all infix operators.**
```r
                    filename=dir("inst/extdata/", full.names=T)[grep("rep", dir("inst/extdata/"))])
                           ~^~
```
[inst/scripts/test_load_data.R:43:61:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L43) *style:* **Put spaces around all infix operators.**
```r
                    filename=dir("inst/extdata/", full.names=T)[grep("rep", dir("inst/extdata/"))])
                                                           ~^~
```
[inst/scripts/test_load_data.R:44:2:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L44) *style:* **Commented code should be removed.**
```r
#se <- summarizeCircs(dir("inst/extdata/", full.names=T)[grep("rep", dir("inst/extdata/"))], wobble=1, colData = cdata)
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:45:45:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L45) *style:* **Put spaces around all infix operators.**
```r
se <- summarizeCircs(colData = cdata, wobble=1)
                                           ~^~
```
[inst/scripts/test_load_data.R:63:2:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L63) *style:* **Commented code should be removed.**
```r
#annot.list <- loadAnnotation("inst/extdata/hsa_ens75_minimal.sqlite")
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:71:27:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L71) *style:* **Put spaces around all infix operators.**
```r
cdata <- data.frame(sample=c("CB1", "CB2", "FC1", "FC2"),
                         ~^~
```
[inst/scripts/test_load_data.R:72:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L72) *style:* **lines should not be more than 80 characters.**
```r
                    filename=c("/data/rajewsky/home/pglazar/projects/ENCODE_brain/human/Cerebellum/rep1/circ_splice_sites.bed",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:72:29:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L72) *style:* **Put spaces around all infix operators.**
```r
                    filename=c("/data/rajewsky/home/pglazar/projects/ENCODE_brain/human/Cerebellum/rep1/circ_splice_sites.bed",
                           ~^~
```
[inst/scripts/test_load_data.R:72:33:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L72) *warning:* **Do not use absolute paths.**
```r
                    filename=c("/data/rajewsky/home/pglazar/projects/ENCODE_brain/human/Cerebellum/rep1/circ_splice_sites.bed",
                                ^~~~~
```
[inst/scripts/test_load_data.R:73:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L73) *style:* **lines should not be more than 80 characters.**
```r
                               "/data/rajewsky/home/pglazar/projects/ENCODE_brain/human/Cerebellum/rep2/circ_splice_sites.bed",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:73:33:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L73) *warning:* **Do not use absolute paths.**
```r
                               "/data/rajewsky/home/pglazar/projects/ENCODE_brain/human/Cerebellum/rep2/circ_splice_sites.bed",
                                ^~~~~
```
[inst/scripts/test_load_data.R:74:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L74) *style:* **lines should not be more than 80 characters.**
```r
                               "/data/rajewsky/home/pglazar/projects/ENCODE_brain/human/FrontalCortex/rep1/circ_splice_sites.bed",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:74:33:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L74) *warning:* **Do not use absolute paths.**
```r
                               "/data/rajewsky/home/pglazar/projects/ENCODE_brain/human/FrontalCortex/rep1/circ_splice_sites.bed",
                                ^~~~~
```
[inst/scripts/test_load_data.R:75:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L75) *style:* **lines should not be more than 80 characters.**
```r
                               "/data/rajewsky/home/pglazar/projects/ENCODE_brain/human/FrontalCortex/rep2/circ_splice_sites.bed"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:75:33:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L75) *warning:* **Do not use absolute paths.**
```r
                               "/data/rajewsky/home/pglazar/projects/ENCODE_brain/human/FrontalCortex/rep2/circ_splice_sites.bed"))
                                ^~~~~
```
[inst/scripts/test_load_data.R:76:2:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L76) *style:* **Commented code should be removed.**
```r
#se <- summarizeCircs(dir("inst/extdata/", full.names=T)[grep("rep", dir("inst/extdata/"))], wobble=1, colData = cdata)
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:77:45:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L77) *style:* **Put spaces around all infix operators.**
```r
se <- summarizeCircs(colData = cdata, wobble=1)
                                           ~^~
```
[inst/scripts/test_load_data.R:89:46:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L89) *style:* **Put spaces around all infix operators.**
```r
se2 <- summarizeCircs(colData = cdata, wobble=1)
                                            ~^~
```
[inst/scripts/test_load_data.R:95:27:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L95) *style:* **Put spaces around all infix operators.**
```r
cdata <- data.frame(sample=c("D0"),
                         ~^~
```
[inst/scripts/test_load_data.R:96:29:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L96) *style:* **Put spaces around all infix operators.**
```r
                    filename="data/Sy5y_D0_sites.bed")
                           ~^~
```
[inst/scripts/test_load_data.R:97:58:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L97) *style:* **Put spaces around all infix operators.**
```r
se <- summarizeCircs(as.character(cdata$filename), wobble=1, colData = cdata)
                                                        ~^~
```
[inst/scripts/test_load_data.R:108:27:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L108) *style:* **Put spaces around all infix operators.**
```r
cdata <- data.frame(sample=c("FC1", "FC2", "H1", "H2", "L1", "L2"),
                         ~^~
```
[inst/scripts/test_load_data.R:109:29:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L109) *style:* **Put spaces around all infix operators.**
```r
                    filename=dir("data/demo/", full.names=T))
                           ~^~
```
[inst/scripts/test_load_data.R:109:58:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L109) *style:* **Put spaces around all infix operators.**
```r
                    filename=dir("data/demo/", full.names=T))
                                                        ~^~
```
[inst/scripts/test_load_data.R:110:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L110) *style:* **lines should not be more than 80 characters.**
```r
se  <- summarizeCircs(circ.files = as.character(cdata$filename), wobble=1, colData = cdata)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:110:72:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L110) *style:* **Put spaces around all infix operators.**
```r
se  <- summarizeCircs(circ.files = as.character(cdata$filename), wobble=1, colData = cdata)
                                                                      ~^~
```
[inst/scripts/test_load_data.R:111:36:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L111) *style:* **Put spaces around all infix operators.**
```r
se1 <- annotateCircs(se, annot.list=annot.list)
                                  ~^~
```
[inst/scripts/test_load_data.R:112:27:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L112) *style:* **Put spaces around all infix operators.**
```r
cdata <- data.frame(sample=c("D0"),
                         ~^~
```
[inst/scripts/test_load_data.R:113:29:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L113) *style:* **Put spaces around all infix operators.**
```r
                    filename="data/Sy5y_D0_sites.bed")
                           ~^~
```
[inst/scripts/test_load_data.R:114:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L114) *style:* **lines should not be more than 80 characters.**
```r
se  <- summarizeCircs(circ.files = as.character(cdata$filename), wobble=1, colData = cdata)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:114:72:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L114) *style:* **Put spaces around all infix operators.**
```r
se  <- summarizeCircs(circ.files = as.character(cdata$filename), wobble=1, colData = cdata)
                                                                      ~^~
```
[inst/scripts/test_load_data.R:115:41:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L115) *style:* **Put spaces around all infix operators.**
```r
se2 <- annotateCircs(se = se, annot.list=annot.list, fixCoordIndexing = TRUE)
                                       ~^~
```
[inst/scripts/test_load_data.R:118:8:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L118) *style:* **Variable and function names should be all lowercase.**
```r
con <- dbConnect(drv    = dbDriver("MySQL"),
       ^~~~~~~~~
```
[inst/scripts/test_load_data.R:118:27:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L118) *style:* **Variable and function names should be all lowercase.**
```r
con <- dbConnect(drv    = dbDriver("MySQL"),
                          ^~~~~~~~
```
[inst/scripts/test_load_data.R:126:7:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L126) *style:* **Variable and function names should be all lowercase.**
```r
ah <- AnnotationHub()
      ^~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:128:11:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L128) *style:* **Variable and function names should be all lowercase.**
```r
gtf.gr <- keepStandardChromosomes(gtf.gr)
          ^~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:129:57:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L129) *style:* **Put spaces around all infix operators.**
```r
seqlevels(gtf.gr) <- paste("chr", seqlevels(gtf.gr), sep="")
                                                       ~^~
```
[inst/scripts/test_load_data.R:131:11:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L131) *style:* **Variable and function names should be all lowercase.**
```r
gtf.gr <- subsetByOverlaps(gtf.gr, rowRanges(se))
          ^~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:131:36:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L131) *style:* **Variable and function names should be all lowercase.**
```r
gtf.gr <- subsetByOverlaps(gtf.gr, rowRanges(se))
                                   ^~~~~~~~~
```
[inst/scripts/test_load_data.R:132:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L132) *style:* **lines should not be more than 80 characters.**
```r
txdb <- makeTxDbFromGRanges(gtf.gr, drop.stop.codons = FALSE, metadata = data.frame(name="Genome", value="GRCh37"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:132:9:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L132) *style:* **Variable and function names should be all lowercase.**
```r
txdb <- makeTxDbFromGRanges(gtf.gr, drop.stop.codons = FALSE, metadata = data.frame(name="Genome", value="GRCh37"))
        ^~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:132:89:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L132) *style:* **Put spaces around all infix operators.**
```r
txdb <- makeTxDbFromGRanges(gtf.gr, drop.stop.codons = FALSE, metadata = data.frame(name="Genome", value="GRCh37"))
                                                                                ~^~
```
[inst/scripts/test_load_data.R:132:105:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L132) *style:* **Put spaces around all infix operators.**
```r
txdb <- makeTxDbFromGRanges(gtf.gr, drop.stop.codons = FALSE, metadata = data.frame(name="Genome", value="GRCh37"))
                                                                                ~^~
```
[inst/scripts/test_load_data.R:133:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L133) *style:* **Variable and function names should be all lowercase.**
```r
saveDb(txdb, file="../data/hsa_ens75_minimal.gtf")
^~~~~~
```
[inst/scripts/test_load_data.R:133:18:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L133) *style:* **Put spaces around all infix operators.**
```r
saveDb(txdb, file="../data/hsa_ens75_minimal.gtf")
                ~^~
```
[inst/scripts/test_load_data.R:136:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L136) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
circ.ends.gr <- rowRanges(se)
^~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:136:17:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L136) *style:* **Variable and function names should be all lowercase.**
```r
circ.ends.gr <- rowRanges(se)
                ^~~~~~~~~
```
[inst/scripts/test_load_data.R:137:7:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L137) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
start(circ.ends.gr) <- end(circ.ends.gr)
      ^~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:137:28:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L137) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
start(circ.ends.gr) <- end(circ.ends.gr)
                           ^~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:139:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L139) *style:* **lines should not be more than 80 characters.**
```r
AnnotateRanges(r1 = circ.ends.gr,         l = annot.list$gene.feats,  null.fact = "intergenic", type="precedence")[1547]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:139:21:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L139) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
AnnotateRanges(r1 = circ.ends.gr,         l = annot.list$gene.feats,  null.fact = "intergenic", type="precedence")[1547]
                    ^~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:139:101:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L139) *style:* **Put spaces around all infix operators.**
```r
AnnotateRanges(r1 = circ.ends.gr,         l = annot.list$gene.feats,  null.fact = "intergenic", type="precedence")[1547]
                                                                                ~^~
```
[inst/scripts/test_load_data.R:140:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L140) *style:* **lines should not be more than 80 characters.**
```r
AnnotateRanges(r1 = circ.ends.gr[1547],   l = annot.list$gene.feats,  null.fact = "intergenic", type="precedence")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:140:21:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L140) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
AnnotateRanges(r1 = circ.ends.gr[1547],   l = annot.list$gene.feats,  null.fact = "intergenic", type="precedence")
                    ^~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:140:101:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L140) *style:* **Put spaces around all infix operators.**
```r
AnnotateRanges(r1 = circ.ends.gr[1547],   l = annot.list$gene.feats,  null.fact = "intergenic", type="precedence")
                                                                                ~^~
```
[inst/scripts/test_load_data.R:144:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L144) *style:* **lines should not be more than 80 characters.**
```r
circs <- lapply(dir("data/demo/", full.names=T)[grep("sites", dir("data/demo/"))], readCircs)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:144:45:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L144) *style:* **Put spaces around all infix operators.**
```r
circs <- lapply(dir("data/demo/", full.names=T)[grep("sites", dir("data/demo/"))], readCircs)
                                           ~^~
```
[inst/scripts/test_load_data.R:145:55:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L145) *style:* **Put spaces around all infix operators.**
```r
circs <- lapply(circs, circLinRatio, return.readcounts=TRUE)
                                                     ~^~
```
[inst/scripts/test_load_data.R:148:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L148) *style:* **lines should not be more than 80 characters.**
```r
circ.files <- dir("/clusterhome/pglazar/projects/circus/ciRcus/data/demo/", full.names=T)[grep("sites", dir("/clusterhome/pglazar/projects/circus/ciRcus/data/demo/"))]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:148:20:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L148) *warning:* **Do not use absolute paths.**
```r
circ.files <- dir("/clusterhome/pglazar/projects/circus/ciRcus/data/demo/", full.names=T)[grep("sites", dir("/clusterhome/pglazar/projects/circus/ciRcus/data/demo/"))]
                   ^~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:148:87:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L148) *style:* **Put spaces around all infix operators.**
```r
circ.files <- dir("/clusterhome/pglazar/projects/circus/ciRcus/data/demo/", full.names=T)[grep("sites", dir("/clusterhome/pglazar/projects/circus/ciRcus/data/demo/"))]
                                                                                ~^~
```
[inst/scripts/test_load_data.R:148:110:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L148) *warning:* **Do not use absolute paths.**
```r
circ.files <- dir("/clusterhome/pglazar/projects/circus/ciRcus/data/demo/", full.names=T)[grep("sites", dir("/clusterhome/pglazar/projects/circus/ciRcus/data/demo/"))]
                                                                                ^~~~~~~~~~~~
```
[inst/scripts/test_load_data.R:149:13:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L149) *style:* **Use <-, not =, for assignment.**
```r
keep.linear = TRUE
            ^
```
[inst/scripts/test_load_data.R:150:8:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L150) *style:* **Use <-, not =, for assignment.**
```r
wobble = 1
       ^
```
[inst/scripts/test_load_data.R:151:6:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L151) *style:* **Use <-, not =, for assignment.**
```r
subs = "all"
     ^
```
[inst/scripts/test_load_data.R:152:12:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L152) *style:* **Use <-, not =, for assignment.**
```r
qualfilter = TRUE
           ^
```
[inst/scripts/test_load_data.R:153:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L153) *style:* **Variable and function names should be all lowercase.**
```r
keepCols = 1:6
^~~~~~~~
```
[inst/scripts/test_load_data.R:153:10:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L153) *style:* **Use <-, not =, for assignment.**
```r
keepCols = 1:6
         ^
```
[inst/scripts/test_load_data.R:154:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L154) *style:* **Variable and function names should be all lowercase.**
```r
colData = NULL
^~~~~~~
```
[inst/scripts/test_load_data.R:154:9:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/inst/scripts/test_load_data.R#L154) *style:* **Use <-, not =, for assignment.**
```r
colData = NULL
        ^
```
[R/annotate.R:12:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L12) *style:* **lines should not be more than 80 characters.**
```r
gtf2sqlite <- function(assembly = c("hg19", "hg38", "mm10", "rn5", "dm6", "WBcel235"), db.file) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:14:9:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L14) *style:* **Variable and function names should be all lowercase.**
```r
  ah <- AnnotationHub()
        ^~~~~~~~~~~~~
```
[R/annotate.R:16:13:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L16) *style:* **Variable and function names should be all lowercase.**
```r
  gtf.gr <- keepStandardChromosomes(gtf.gr)
            ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:16:13:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L16) *warning:* **no visible global function definition for 'keepStandardChromosomes'**
```r
  gtf.gr <- keepStandardChromosomes(gtf.gr)
            ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:17:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L17) *warning:* **no visible global function definition for 'seqlevels<-'**
```r
  seqlevels(gtf.gr) <- paste("chr", seqlevels(gtf.gr), sep="")
  ^~~~~~~~~
```
[R/annotate.R:17:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L17) *warning:* **no visible global function definition for 'seqlevels'**
```r
  seqlevels(gtf.gr) <- paste("chr", seqlevels(gtf.gr), sep="")
  ^~~~~~~~~
```
[R/annotate.R:17:59:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L17) *style:* **Put spaces around all infix operators.**
```r
  seqlevels(gtf.gr) <- paste("chr", seqlevels(gtf.gr), sep="")
                                                         ~^~
```
[R/annotate.R:18:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L18) *warning:* **no visible global function definition for 'seqlevels'**
```r
  seqlevels(gtf.gr)[which(seqlevels(gtf.gr) == "chrMT")] <- "chrM"
  ^~~~~~~~~
```
[R/annotate.R:18:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L18) *warning:* **no visible global function definition for 'seqlevels'**
```r
  seqlevels(gtf.gr)[which(seqlevels(gtf.gr) == "chrMT")] <- "chrM"
  ^~~~~~~~~
```
[R/annotate.R:18:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L18) *warning:* **no visible global function definition for 'seqlevels<-'**
```r
  seqlevels(gtf.gr)[which(seqlevels(gtf.gr) == "chrMT")] <- "chrM"
  ^~~~~~~~~
```
[R/annotate.R:19:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L19) *style:* **lines should not be more than 80 characters.**
```r
  txdb <- makeTxDbFromGRanges(gtf.gr, drop.stop.codons = FALSE, metadata = data.frame(name="Genome", value=assembly))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:19:11:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L19) *style:* **Variable and function names should be all lowercase.**
```r
  txdb <- makeTxDbFromGRanges(gtf.gr, drop.stop.codons = FALSE, metadata = data.frame(name="Genome", value=assembly))
          ^~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:19:91:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L19) *style:* **Put spaces around all infix operators.**
```r
  txdb <- makeTxDbFromGRanges(gtf.gr, drop.stop.codons = FALSE, metadata = data.frame(name="Genome", value=assembly))
                                                                                ~^~
```
[R/annotate.R:19:107:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L19) *style:* **Put spaces around all infix operators.**
```r
  txdb <- makeTxDbFromGRanges(gtf.gr, drop.stop.codons = FALSE, metadata = data.frame(name="Genome", value=assembly))
                                                                                ~^~
```
[R/annotate.R:20:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L20) *style:* **Variable and function names should be all lowercase.**
```r
  saveDb(txdb, file=db.file)
  ^~~~~~
```
[R/annotate.R:20:20:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L20) *style:* **Put spaces around all infix operators.**
```r
  saveDb(txdb, file=db.file)
                  ~^~
```
[R/annotate.R:36:11:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L36) *style:* **Variable and function names should be all lowercase.**
```r
  txdb <- loadDb(txdb.file)
          ^~~~~~
```
[R/annotate.R:37:18:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L37) *warning:* **no visible global function definition for 'exons', Did you mean 'exns'?**
```r
  exns <- unique(exons(txdb))
                 ^~~~~
```
[R/annotate.R:43:17:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L43) *style:* **Variable and function names should be all lowercase.**
```r
  gene.feats <- GRangesList(cds    = reduce(cds(txdb)),
                ^~~~~~~~~~~
```
[R/annotate.R:44:52:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L44) *style:* **Variable and function names should be all lowercase.**
```r
                            utr5   = reduce(unlist(fiveUTRsByTranscript(txdb))),
                                                   ^~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:45:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L45) *style:* **lines should not be more than 80 characters.**
```r
                            utr3   = reduce(unlist(threeUTRsByTranscript(txdb))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:45:52:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L45) *style:* **Variable and function names should be all lowercase.**
```r
                            utr3   = reduce(unlist(threeUTRsByTranscript(txdb))),
                                                   ^~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:46:52:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L46) *style:* **Variable and function names should be all lowercase.**
```r
                            intron = reduce(unlist(intronsByTranscript(txdb))),
                                                   ^~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:48:16:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L48) *style:* **Variable and function names should be all lowercase.**
```r
  junctions <- GRangesList(start = junct.start,
               ^~~~~~~~~~~
```
[R/annotate.R:76:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L76) *style:* **lines should not be more than 80 characters.**
```r
                    assembly = c("hg19", "hg38", "mm10", "rn5", "dm6", "WBcel235"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:77:21:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L77) *style:* **Variable and function names should be all lowercase.**
```r
                    fixCoordIndexing=TRUE,
                    ^~~~~~~~~~~~~~~~
```
[R/annotate.R:84:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L84) *style:* **lines should not be more than 80 characters.**
```r
          function(se, annot.list, assembly = c("hg19", "hg38", "mm10", "rn5", "dm6", "WBcel235"), fixCoordIndexing = TRUE, ...) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:84:100:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L84) *style:* **Variable and function names should be all lowercase.**
```r
          function(se, annot.list, assembly = c("hg19", "hg38", "mm10", "rn5", "dm6", "WBcel235"), fixCoordIndexing = TRUE, ...) {
                                                                                ^~~~~~~~~~~~~~~~
```
[R/annotate.R:86:17:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L86) *style:* **Variable and function names should be all lowercase.**
```r
            if (fixCoordIndexing == TRUE) {
                ^~~~~~~~~~~~~~~~
```
[R/annotate.R:87:23:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L87) *style:* **Only use double-quotes.**
```r
              message('checking out coordinate indexing...')
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:88:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L88) *style:* **lines should not be more than 80 characters.**
```r
              coordfix <- testCoordinateIndexing(rowRanges(se), annot.list$gene.feats$cds)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:88:50:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L88) *style:* **Variable and function names should be all lowercase.**
```r
              coordfix <- testCoordinateIndexing(rowRanges(se), annot.list$gene.feats$cds)
                                                 ^~~~~~~~~
```
[R/annotate.R:89:62:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L89) *style:* **Put spaces around all infix operators.**
```r
              tophits <- sapply(coordfix, function(x) which(x/sum(x) > 0.9))
                                                            ~^~
```
[R/annotate.R:90:48:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L90) *style:* **Put spaces around all infix operators.**
```r
              if (!is.na(max(coordfix[[1]][2:3]/sum(coordfix[[1]])) > 0.9) &
                                              ~^~
```
[R/annotate.R:91:41:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L91) *style:* **Put spaces around all infix operators.**
```r
                  max(coordfix[[1]][2:3]/sum(coordfix[[1]])) > 0.9) {
                                       ~^~
```
[R/annotate.R:100:48:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L100) *style:* **Put spaces around all infix operators.**
```r
              if (!is.na(max(coordfix[[2]][2:3]/sum(coordfix[[2]])) > 0.9) &
                                              ~^~
```
[R/annotate.R:101:41:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L101) *style:* **Put spaces around all infix operators.**
```r
                  max(coordfix[[2]][2:3]/sum(coordfix[[2]])) > 0.9) {
                                       ~^~
```
[R/annotate.R:110:38:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L110) *style:* **Variable and function names should be all lowercase.**
```r
              testCoordinateIndexing(rowRanges(se), annot.list$gene.feats$cds)
                                     ^~~~~~~~~
```
[R/annotate.R:115:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L115) *style:* **lines should not be more than 80 characters.**
```r
            if (!any(seqlevelsStyle(annot.list$genes) %in% seqlevelsStyle(se))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:115:22:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L115) *style:* **Variable and function names should be all lowercase.**
```r
            if (!any(seqlevelsStyle(annot.list$genes) %in% seqlevelsStyle(se))) {
                     ^~~~~~~~~~~~~~
```
[R/annotate.R:115:60:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L115) *style:* **Variable and function names should be all lowercase.**
```r
            if (!any(seqlevelsStyle(annot.list$genes) %in% seqlevelsStyle(se))) {
                                                           ^~~~~~~~~~~~~~
```
[R/annotate.R:116:23:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L116) *style:* **Only use double-quotes.**
```r
              warning('nonmatching seqlevel styles, will fix automatically')
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:118:17:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L118) *style:* **Variable and function names should be all lowercase.**
```r
                seqlevelsStyle(annot.list[[i]]) <- seqlevelsStyle(se)
                ^~~~~~~~~~~~~~
```
[R/annotate.R:118:52:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L118) *style:* **Variable and function names should be all lowercase.**
```r
                seqlevelsStyle(annot.list[[i]]) <- seqlevelsStyle(se)
                                                   ^~~~~~~~~~~~~~
```
[R/annotate.R:122:21:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L122) *style:* **Only use double-quotes.**
```r
            message('annotating host genes...')
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:124:21:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L124) *style:* **Only use double-quotes.**
```r
            message('annotating splice junctions...')
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:129:23:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L129) *style:* **Only use double-quotes.**
```r
              message('calculating circular/linear ratios...')
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:132:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L132) *style:* **lines should not be more than 80 characters.**
```r
              message('no linear splicing info found, skipping circular/linear ratios...')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:132:23:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L132) *style:* **Only use double-quotes.**
```r
              message('no linear splicing info found, skipping circular/linear ratios...')
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:152:15:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L152) *style:* **Variable and function names should be all lowercase.**
```r
  circs.gr <- rowRanges(se)
              ^~~~~~~~~
```
[R/annotate.R:153:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L153) *style:* **lines should not be more than 80 characters.**
```r
  circs.gr$id <- paste0(seqnames(circs.gr), ":", start(circs.gr), "-", end(circs.gr))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:154:5:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L154) *style:* **Commented code should be removed.**
```r
  # circs.gr <- sort(circs.gr)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:158:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L158) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
  circ.starts.gr <- circs.gr
  ^~~~~~~~~~~~~~
```
[R/annotate.R:159:7:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L159) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
  end(circ.starts.gr) <- start(circ.starts.gr)
      ^~~~~~~~~~~~~~
```
[R/annotate.R:159:32:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L159) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
  end(circ.starts.gr) <- start(circ.starts.gr)
                               ^~~~~~~~~~~~~~
```
[R/annotate.R:160:3:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L160) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
  circ.ends.gr <- circs.gr
  ^~~~~~~~~~~~
```
[R/annotate.R:161:9:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L161) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
  start(circ.ends.gr) <- end(circ.ends.gr)
        ^~~~~~~~~~~~
```
[R/annotate.R:161:30:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L161) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
  start(circ.ends.gr) <- end(circ.ends.gr)
                             ^~~~~~~~~~~~
```
[R/annotate.R:163:17:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L163) *style:* **Variable and function names should be all lowercase.**
```r
  olap.start <- findOverlaps(circ.starts.gr, genes.gr, type="within")
                ^~~~~~~~~~~~
```
[R/annotate.R:163:30:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L163) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
  olap.start <- findOverlaps(circ.starts.gr, genes.gr, type="within")
                             ^~~~~~~~~~~~~~
```
[R/annotate.R:163:60:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L163) *style:* **Put spaces around all infix operators.**
```r
  olap.start <- findOverlaps(circ.starts.gr, genes.gr, type="within")
                                                          ~^~
```
[R/annotate.R:164:17:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L164) *style:* **Variable and function names should be all lowercase.**
```r
  olap.end   <- findOverlaps(circ.ends.gr, genes.gr, type="within")
                ^~~~~~~~~~~~
```
[R/annotate.R:164:30:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L164) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
  olap.end   <- findOverlaps(circ.ends.gr, genes.gr, type="within")
                             ^~~~~~~~~~~~
```
[R/annotate.R:164:58:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L164) *style:* **Put spaces around all infix operators.**
```r
  olap.end   <- findOverlaps(circ.ends.gr, genes.gr, type="within")
                                                        ~^~
```
[R/annotate.R:166:4:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L166) *style:* **Commented code should be removed.**
```r
  #circs$id <- paste(circs$chrom, ":", circs$start, "-", circs$end, sep="")
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:167:56:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L167) *style:* **Variable and function names should be all lowercase.**
```r
  circs <- data.table(start.hit = names(circs.gr) %in% queryHits(olap.start),
                                                       ^~~~~~~~~
```
[R/annotate.R:168:56:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L168) *style:* **Variable and function names should be all lowercase.**
```r
                      end.hit   = names(circs.gr) %in% queryHits(olap.end),
                                                       ^~~~~~~~~
```
[R/annotate.R:172:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L172) *style:* **lines should not be more than 80 characters.**
```r
  matches.start <- data.table(id=circs.gr$id[queryHits(olap.start)], gene=names(genes.gr)[subjectHits(olap.start)] )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:172:33:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L172) *style:* **Put spaces around all infix operators.**
```r
  matches.start <- data.table(id=circs.gr$id[queryHits(olap.start)], gene=names(genes.gr)[subjectHits(olap.start)] )
                               ~^~
```
[R/annotate.R:172:46:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L172) *style:* **Variable and function names should be all lowercase.**
```r
  matches.start <- data.table(id=circs.gr$id[queryHits(olap.start)], gene=names(genes.gr)[subjectHits(olap.start)] )
                                             ^~~~~~~~~
```
[R/annotate.R:172:74:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L172) *style:* **Put spaces around all infix operators.**
```r
  matches.start <- data.table(id=circs.gr$id[queryHits(olap.start)], gene=names(genes.gr)[subjectHits(olap.start)] )
                                                                        ~^~
```
[R/annotate.R:172:91:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L172) *style:* **Variable and function names should be all lowercase.**
```r
  matches.start <- data.table(id=circs.gr$id[queryHits(olap.start)], gene=names(genes.gr)[subjectHits(olap.start)] )
                                                                                ^~~~~~~~~~~
```
[R/annotate.R:173:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L173) *style:* **lines should not be more than 80 characters.**
```r
  matches.end   <- data.table(id=circs.gr$id[queryHits(olap.end)],   gene=names(genes.gr)[subjectHits(olap.end)] )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:173:33:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L173) *style:* **Put spaces around all infix operators.**
```r
  matches.end   <- data.table(id=circs.gr$id[queryHits(olap.end)],   gene=names(genes.gr)[subjectHits(olap.end)] )
                               ~^~
```
[R/annotate.R:173:46:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L173) *style:* **Variable and function names should be all lowercase.**
```r
  matches.end   <- data.table(id=circs.gr$id[queryHits(olap.end)],   gene=names(genes.gr)[subjectHits(olap.end)] )
                                             ^~~~~~~~~
```
[R/annotate.R:173:74:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L173) *style:* **Put spaces around all infix operators.**
```r
  matches.end   <- data.table(id=circs.gr$id[queryHits(olap.end)],   gene=names(genes.gr)[subjectHits(olap.end)] )
                                                                        ~^~
```
[R/annotate.R:173:91:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L173) *style:* **Variable and function names should be all lowercase.**
```r
  matches.end   <- data.table(id=circs.gr$id[queryHits(olap.end)],   gene=names(genes.gr)[subjectHits(olap.end)] )
                                                                                ^~~~~~~~~~~
```
[R/annotate.R:175:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L175) *style:* **lines should not be more than 80 characters.**
```r
  start.list <- lapply(split(matches.start, matches.start$id), function(x) x$gene)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:176:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L176) *style:* **lines should not be more than 80 characters.**
```r
  end.list   <- lapply(split(matches.end,   matches.end$id),   function(x) x$gene)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:178:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L178) *style:* **lines should not be more than 80 characters.**
```r
  circs <- merge(circs, data.table(id=names(start.list), starts=sapply(start.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:178:38:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L178) *style:* **Put spaces around all infix operators.**
```r
  circs <- merge(circs, data.table(id=names(start.list), starts=sapply(start.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
                                    ~^~
```
[R/annotate.R:178:64:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L178) *style:* **Put spaces around all infix operators.**
```r
  circs <- merge(circs, data.table(id=names(start.list), starts=sapply(start.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
                                                              ~^~
```
[R/annotate.R:178:113:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L178) *style:* **Put spaces around all infix operators.**
```r
  circs <- merge(circs, data.table(id=names(start.list), starts=sapply(start.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
                                                                                ~^~
```
[R/annotate.R:178:124:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L178) *style:* **Put spaces around all infix operators.**
```r
  circs <- merge(circs, data.table(id=names(start.list), starts=sapply(start.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
                                                                                ~^~
```
[R/annotate.R:178:136:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L178) *style:* **Put spaces around all infix operators.**
```r
  circs <- merge(circs, data.table(id=names(start.list), starts=sapply(start.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
                                                                                ~^~
```
[R/annotate.R:179:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L179) *style:* **lines should not be more than 80 characters.**
```r
  circs <- merge(circs, data.table(id=names(end.list), ends=sapply(end.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/annotate.R:179:38:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L179) *style:* **Put spaces around all infix operators.**
```r
  circs <- merge(circs, data.table(id=names(end.list), ends=sapply(end.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
                                    ~^~
```
[R/annotate.R:179:60:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L179) *style:* **Put spaces around all infix operators.**
```r
  circs <- merge(circs, data.table(id=names(end.list), ends=sapply(end.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
                                                          ~^~
```
[R/annotate.R:179:107:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L179) *style:* **Put spaces around all infix operators.**
```r
  circs <- merge(circs, data.table(id=names(end.list), ends=sapply(end.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
                                                                                ~^~
```
[R/annotate.R:179:118:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L179) *style:* **Put spaces around all infix operators.**
```r
  circs <- merge(circs, data.table(id=names(end.list), ends=sapply(end.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
                                                                                ~^~
```
[R/annotate.R:179:130:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L179) *style:* **Put spaces around all infix operators.**
```r
  circs <- merge(circs, data.table(id=names(end.list), ends=sapply(end.list, function(x) paste(x, collapse=","))), by="id", all.x=T)
                                                                                ~^~
```
[R/annotate.R:186:4:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L186) *style:* **Commented code should be removed.**
```r
  #ptm <- proc.time()
   ^~~~~~~~~~~~~~~~~~
```
[R/annotate.R:192:1:](https://github.com/BIMSBbioinfo/ciRcus/blob/8c436f429d4a81cf0f4dbb9737ceb2248aef5fc1/R/annotate.R#L192) *style:* **lines should not be more than 80 characters.**
```r
    tmpgenes <- append(tmpgenes, paste(hs[[circ]][hs[[circ]] %in% he[[circ]]], collapse=","))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


self тут лишний, он нужен только при присваивании занчений через сеттеры.


updating existing notification icon not working, will fix later when at home again


`error C2143: syntax error: missing ')' before ';'`

A missing `)`. Please try to compile before pushing.


Можно в строку несколько атрибутов объявить `attr_reader :trains, :name`


Thanks! I will submit a PR later this day.

@locutus2 Well, tuning is all about probabilities. The result simply reflects how often we win with 5 pawns or with 3 pawns left. One may not like this discontinuity, but it gains elo.


@jaraco we could use `constraints.txt` (although I don't like the approach of having multiple places of dependencies declarations) and install deps using smth like `pip install -c constraints.txt -e .`, but I'm not sure whether `tox` is able to encapsulate this option. Any ideas?


Это не хеш должен быть, а массив


Аргумент можно назвать просто name, мы и так с классом Station работаем, понятно, что мы не имя маршрута тут задаем


Ditto missing `)`.


self можно убрать везде по коду, кроме присваиваний. Так код станет "легче"


@willrstern Code was never just code...


Объявляй атрибуты в строку


Что такое длина поезда? Кол-во вагонов? Тогда так и назови - wagons_count


Лучше хранить индекс станции, а не саму станцию, тогда перемещение - это просто изменение индекса на +/- 1


Лучше назвать "добавить вагон"


Удалить вагон


self лишний. И если вагонов 0, что тогда?


по заданию, перемещение поезда возможно вперед и назад только на 1 станцию за раз. И лучше сделать 2 разных метода для перемещения вперед и назад


oh yeah, real mature u guys


Чтобы не искать индекс по станции, проще сразу хранить индекс


сделай отдельные методы для показа текущей/предыдущей/следующей станции


Great work Fabian :)


这句不要可以吗…


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f2f26a42fcb8f71329dbabcdf3b1c99e2211e157	@dortal


Отделяй блок атрибутов от методов пустой строкой


不禁


Отделяй методы друг от друга пустой строкой


Could we not directly embed the f template inside sequencify and remove type altogether?


Можно сделать атрибут-геттер для этого. И лучше назвать его просто trains


what's the reason to drop maildir widget?


Зачем хранить станции отдельно, да еще и в массивах из 1-го элемента, когда можно сразу хранить все станции, и начальную и конечную и промежуточные, в одном массиве?


My motivation is to have only LF line endings in the repo. Perhaps I'm missing smth, but as I understand this would guarantee having `LF` for all new files committed to the repo and unchanged line endings for existing files across OSs. That it why I don't really get your concern.


пустые строки между методами


В этом методе отпадет необходмость, если все хранить  в одном массиве и сделать для него геттер


Не нужно никакого форматрирвания, пусть об этом заботится вызывающий код, а методы пусть просто возвращают данные, что с ними делать - не их забота.


Done removing commented codes on this file[home.app.blade].


поправил


![](https://github.trello.services/images/mini-trello-icon.png) [CITYBUR-13](https://trello.com/c/yVFsGVUD/24-citybur-13)


![](https://github.trello.services/images/mini-trello-icon.png) [CITYBUR-03](https://trello.com/c/yeEvYTDd/14-citybur-03)


Good. Now compilation works under Linux with sources from GitHub, but executable still requires folder "russian" with translated wad files from binary archive.

Never stop learning. Next step - translation of remaining strings for proper console output.


Не нужно объявлять переменные без значений, их можно просто начать использовать в любом месте, они по-умолчанию инициализируются как nil


А вставлять промежуточные станции можно методом `insert`


这句是不是想去掉的……


А если вагонов еще нет? Будет отрицательное кол-во


Just to summarise the patches I needed for this to compile:
```c
--- a/tests/findalldevstest.c 2017-03-12 10:07:31
+++ b/tests/findalldevstest.c 2017-03-12 11:18:56
@@ -23,6 +23,8 @@
 static char *iptos(bpf_u_int32 in);

 #ifdef _WIN32
+#include "portability.h"
+
 /*
  * Generate a string for a Win32-specific error (i.e. an error generated when
  * calling a Win32 API).
@@ -59,6 +61,7 @@
   HANDLE console_handle = GetStdHandle(STD_INPUT_HANDLE);
   DWORD console_mode, save_console_mode;
   static char password[128+1];
+  char *p;

   fprintf(stderr, "%s", prompt);

@@ -67,17 +70,17 @@
    */
   if (!GetConsoleMode(console_handle, &console_mode)) {
     fprintf(stderr, "Can't get console mode: %s\n",
-            win32_strerror(GetLastError());
+            win32_strerror(GetLastError()));
     exit(1);
   }
   save_console_mode = console_mode;
   console_mode &= ~ENABLE_ECHO_INPUT;
   if (!SetConsoleMode(console_handle, console_mode)) {
     fprintf(stderr, "Can't set console mode: %s\n",
-            win32_strerror(GetLastError());
+            win32_strerror(GetLastError()));
     exit(1);
   }
-  if (fgets(username, sizeof username, stdin) == NULL) {
+  if (fgets(password, sizeof password, stdin) == NULL) {
     fprintf(stderr, "\n");
     SetConsoleMode(console_handle, save_console_mode);
     exit(1);
```


по заданию, перемещение поезда возможно вперед и назад только на 1 станцию за раз.


А если маршрут еще не указан?


There is generic implementation at main mir repo https://github.com/libmir/mir/blob/master/source/mir/glas/l1.d

BTW, you are well come to contribute to Mir GLAS and other mir repos.


Thank you for the comments, would you like to make a pull request with the fixes?

Guy's main working copy is on macOS, my main working copy is on Linux. Travis CI covers both and now tests the rpcap too (see the most recent build status for libpcap), there are also Linux and Solaris buildbots. Do you know any simple way to run a Windows build?


Чтобы не искать индекс по станции, проще сразу хранить индекс


сделай отдельные методы для показа текущей/предыдущей/следующей станции


BTW, if `pcap_win32strerror()` was exported and part of the API, that could maybe have been used instead?


Werewolf for Telegram/Werewolf Node/Werewolf.cs

What if the alive player belongs to wolf team?


That all compiles OK for me now, thanks.


А как ты сравниваешь объект и его номер? До этого было правильно


Не нужны тут переменные класса. Они же будут на все объекты одинаковыми. И переместив один поезд, ты переместишь вообще все.


А как поезд будет перемещаться назад по маршруту?


A `)` too much:
```
 				if (pkt_header->ts.tv_sec < pw->samp_time.tv_sec ||
-				   (pkt_header->ts.tv_sec == pw->samp_time.tv_sec) && pkt_header->ts.tv_usec < pw->samp_time.tv_usec)) {
+				   (pkt_header->ts.tv_sec == pw->samp_time.tv_sec) && pkt_header->ts.tv_usec < pw->samp_time.tv_usec) {
 					bp += Packet_WORDALIGN(caplen + hdrlen);
 					continue;
```


Вообще, сам метод решения не очень хороший, т.к тут дважды перебор, а в первом решении только один раз, поэтому оно лучше


A missing `>`:
```
 				 * delivered to our caller, so let's update
 				 * the target time.
 				 */
-				pw-samp_time.tv_usec = pkt_header->ts.tv_usec + p->rmt_samp.value * 1000;
+				pw->samp_time.tv_usec = pkt_header->ts.tv_usec + p->rmt_samp.value * 1000;
```


Are you sure that you would completely overwrite the history stats information in score<QUIETS>? That is very valuable information


29 февраля тоже дает +1 к дню, не только с марта действует это правило. Вообще, лучше было бы сначала объявить массив дней, а потом поменять значение для февраля, если год високосный. Остальной алгоритм был бы тем же самым, что и для не високосного.


add register


I wonder why you need to change it?


it should still be used ? The code (tries to) implement
m.value = a*m.value+b
or do I understand incorrectly your question.


use `if (!strcmp(name, "")) {`


Sorry forgot it! i have overloked the m.value on the right side.


Did you check what line exactly causes the segfault?


Да вообще не нужно объявлять переменные, которые не инициализируются. Просто используй их в тот момент, когда нужно. Они появятся автоматически и будут равны nil.


Почему "или", тут же "и": поезд остановлен И у него есть вагоны


Вообще, лучше raise вынести в начало метода:

```
raise ... if @speed != 0
raise ... if @n_cars == 0

@n_cars -= 1
```


睡眠数据丢失问题解决了？？darkwake=0就行了？


Я немного подкорректировал задание, это подразумевалось, но увидев твое решение, понял, что нужно явно указать: нужно, чтобы поезд перемещался на 1 станцию за раз. Он может перемещаться впреед и назвад (разные методы), но на 1 станцию в маршруте, а не на произвольную


Странно, я это сразу исправил когда начал в departure передавать объект
Видимо я что-то с git ошибся и изменения не запушил


Remote connections are already in Enable/DisableRemoteAssistance and Enable/DisableRemoteDesktop. Moreover the registry paths in this commit are not correct.


Раз у тебя в переменной хранится индекс, то и отрази это в названии переменной, чтобы не было путаницы, т.к. можно подумать, что там объект


Почему тут используется 0,  а не переменная, в которой задан индекс?


This is what I mean:

```
C:\Users\jaraco> git clone gh://cherrypy/cheroot
Cloning into 'cheroot'...
remote: Counting objects: 25783, done.
remote: Compressing objects: 100% (77/77), done.
remote: Total 25783 (delta 35), reused 0 (delta 0), pack-reused 25706
Receiving objects: 100% (25783/25783), 27.69 MiB | 10.56 MiB/s, done.
Resolving deltas: 100% (5029/5029), done.

C:\Users\jaraco> cd cheroot
C:\Users\jaraco\cheroot> python
Python 3.6.0 (v3.6.0:41df79263a11, Dec 23 2016, 08:06:12) [MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> with open('setup.py', 'rb') as setup:
...   print(next(setup))
...
b'import io\r\n'
```

So even though LF is used in the repo, the 'text' magic causes CRLF on Windows checkouts. And if that checkout happens to be on a shared filesystem with a Unix machine, that Unix machine gets CRLF line endings also.


А я неправильно обозвал переменную которую передаю в метод и Вас запутал наверно.
В метод передается объект, в массиве тоже объекты, они сравниваются. Или что то все таки неправильно?


Oh... I see. I think I could be able to fix this, let me check git docs again)


does this change affects running lr-ppsspp emulator on armv7 ? I have problem with running this emulator on osmc


О, наверно надо будет сделать реверс массива маршрута чтобы поезд курировал между станциями. Просто в задании написано что маршрут присваивается поезду и я думал что после того как поезд заканчивает путь он должен принять новый маршрут.
Я доделаю функционал


Should still explain what it does, and you left out docs for `frame:Disable()`


fixed, thx ;)


* Логика верная, но тут есть баг: в текущей реализации будут счиаться инстансы всех классов, куда подключен модуль. Например, если он подключен к поездам и станциями, то создание станции будет увеличивать счетчик поездаов и наоборот. А так быть не должно. Это происходит потому что ты используешь переменные класса (@@instance_counter) но на уровне модуля, а сам модуль подключается через extend. Когда модуль подключается через exetnd, его инстанс-методы становятся методами класса, куда модуль подключен, а инстанс-переменные - переменными класса. Но т.к. у тебя используется сразу класс-переменная, то она становится класс-переменной уровня модуля, т.е. как бы глобальной для всех классов, куда подключен модуль. Это можно еще представить наследованием: когда мы модуль подключаем, он добавляется как базовый класс в цепочку наследования и раз ты используешь класс-переменные уровня модуля, то она становистя общей для всех классов-наследников. Решение: нужно использовать инстанс-переменную, можно даже через attr_accessor.


А зачем тогда вообще тебе ClassMethods, если ты работаешь с переменной внутри InstanceMethods?


Слишком длинное название, достаточно `company` или `manufacturer`


This breaks the base installation. That \ in sed command was escaping space, now it escapes the $. Fixing now...


"Used to make a function or a table of functions available to all unit frames as methods."


Тут лучше хранить в хеше, где ключ - номер, а значение - объект


Ого, значит использование переменных класса я видимо неправильно понял. =)
Сейчас дошло что я натворил =)


Если использовать хеш, методо будет гораздо эффективнее


just a test , last year just use github,but not really know how it works,l


Пиздато что с белым фоном)))


This commit is a very very nice one. gr8 one keep on.

i am working one myself can you help me.

love encaflix1


I just realised that "Reduce boot.img size" doesn't even belong here. What was I thinking........


c'était @chataigne73 mais ça fonctionné pas le '.+?&' pour le site ou il avait le soucis


Does it really take a table?


Looks like this works - https://travis-ci.org/cherrypy/cherrypy/jobs/210232113

It relies on a newer form of the dependencies declarations, though, so might have compatibility implications for older versions of setuptools or pip.


Такие вещи проще из Stylish смотреть чем ждать пока там на транке сбилдится.


Don't do this. This is a huge mistake.


ok :smile:


we could also remove:
+  <ItemGroup Condition=" '$(TargetFramework)' == 'uap10.0' ">
 +    <PackageReference Include="System.Net.Http" Version="4.1.0" />
 +    <PackageReference Include="System.Dynamic.Runtime" Version="4.0.11" />
 +    <PackageReference Include="System.Linq" Version="4.1.0" />
 +  </ItemGroup>

from the project file, not sure if you left it in for some reason


Верни деньги


"string of macro conditional(s) which defines when to display the header", then add a link to a document detailing these, should be good enough.
We might have to create that document ourselves though.


@jaraco LGTM


"Array containing all unit frames spawned with `oUF:Spawn()`"


"Table containing all headers spawned with `oUF:SpawnHeader()`"


Назови переменную `@current_station_index`, чтобы было ясно, что там индекс, а не станция.


![](https://github.trello.services/images/mini-trello-icon.png) [CITYBUR-15](https://trello.com/c/tBErqJK8/27-citybur-15)


FIxed


сделал


@cherja измени название на англ


ok


Great.


this commit makes a regression with after burner climax. previous build only had texture error with player's airplane. now there is only black screen with some menu around the screen visible.


Lines 188,189,190,191: users who need privacy shouldn't be forced to use Google DNS
Line 268: this line reduces screen quality on older devices so far I've heard to alleviate stress on the GPU of older phones. On op2, it produces no visible benefit and reduces screen quality

Everything else looks pretty good, good job on the commit title and can't really find fault with the rest


hello world in c programming language


Yes, AppVeyor rocks for MSVC. It needs a set of up-to-date `*.sln`+ `*.vcxproj`  files.
But  I'm not sure the one in `Win32/Prj` are a good candidate; They don't build any `tests/*.c`  files and are very NPcap centric.

Anyway, I've used `appveyor.yml` in some other projects. I could simply contain:
```
build_script:
    - cd Win32\Prj
    - msbuild -nologo -p:Configuration=Release wpcap.sln
    - msbuild -nologo -p:Configuration=Release tests.sln
    - findalldevstest
```
I'm not sure `findalldevstest` would give any output (since AppVeyor probably doesn't have WinPcap installed), but it would test the `link` stage etc.


let sdo it


I don't really know his anti cheat system, but there's a difference in 4.3.4 and 3.3.5. But still, getting an okay passive anti cheat isn't that hard (it will have many false positives though) - there are even some public as you mention, but getting a well done one is another thing.

While that's said, there are many Todo's for 434, and it seems to only be Frank working public on the repository.


Thank you!


This patch is not correct. I also wasn't the original source for the xml, it was @Rapper_skull from xda/Open GApps. Use the Open GApps official patch set: http://opengapps.org/blog/post/2016/10/06/nougat-webview/


People are still merging this various places so I'm going to leave this note here as well..

This patch is not correct. I also wasn't the original source for the xml, it was @Rapper_skull from xda/Open GApps. Use the Open GApps official patch set: http://opengapps.org/blog/post/2016/10/06/nougat-webview/


![](https://github.trello.services/images/mini-trello-icon.png) [Создать пустую вьюху для /Admin/Containers(см /Admin/Categories)](https://trello.com/c/Lx7ikIHa/53-admin-containers-admin-categories)


![](https://github.trello.services/images/mini-trello-icon.png) [Сделать метод /Admin/Containers](https://trello.com/c/RJdx4ybD/40-admin-containers)


Hello, is lz4 not already the default compression algorithm?
https://github.com/flar2/kernel-msm/blob/a0c2059613e2b2695c4458dc89ce79c36d02c419/arch/arm/configs/elementalx_defconfig#L1219
https://github.com/flar2/kernel-msm/blob/ElementalX-1.00/drivers/block/zram/Kconfig#L18


// [GS] IMHO popis parametru by mel byt v stejnem radku s parametrem
// [DONE] upravit vsude, i v tride Token
// [GS] Asi chceme porovnat hodnoty misto referenci.
// [TODO] mame pridat JavaDoc?
// [GS] Nazev promenne 'r' jsem vymenil na 'oldTop'.
// [GS] Meli bychom pouzivat vzdy slozene zavorky i u jednoradkovych if-else. Nekdy pouzivame nekdy ne.
// [TODO] indentLvl nebo pouze indent?
// [TODO] Nazev promenne 'min' na 'prevMin'?
// [GS] Zmena nazvu metody.
// [GS] pridani zavorek k podmince
// [GS] Porovnani hodnot misto referenci.
// [TODO] tato verze?
/* [TODO] nebo tato?
// [GS] Netreba mit strednik na konci tridy.
// [TODO] Zhodnout se na nazvu.
// [TODO] nahradit dlouhou podminku boolean promenou?
// [TODO] Nazev promenne?
// [GS] Equals misto !=
// [DONE] tady dava smysl i for cyklus, ale nevim, jestli while neni lepsi
// [GS] while podle mne je prehlednejsi
// [GS] Zmena poradi parametru
// [DONE] zase, mozna je lepsi predelat na while, nevim
// [GS] while podle mne je prehlednejsi
// [GS] Zmena poradi parametru
// [GS] Jmeno promenne 'l' na 'level'.
// [TODO] (int) je imho zbytecny
// [GS] Pridani {}
// [GS] Presunuti do if-u. Pokud je start.next null, pak start.next.flags hodi NullPointerException
// [TODO] ZKONTROLOVAT!
// [GS] Pridani {}
// [DONE] tady asi for cyklus docela dava smysl
// [GS] Zavorky {}
// [GS] Prejmenovani 't' na 'prev'
// [GS] 'else if' misto 'else' a 'if'
// [GS] Zavorky {}
// [TODO] prejmenovat 't', ale na co??


Where is this?


This changes has been tested


No, but you can check it yourself, just run tests (see https://github.com/bdellegrazie/lualdap/pull/2).


i'd say for sanity's sake @jun325 you should be free to update the minor and patch numbers of the version (a la http://semver.org/) - starting at this point, so let's call the next release (with the changes here up to now) 2.0.1 (and the next patch 2.0.2, and if adding an actual new feature/button/etc 2.1.0)

@stevefaulkner confirm that this is ok (seems non-controversial to me)


we dont even use that lol


tested


and i think going forward (assuming we do much more in future in terms of aviewer development) let's coordinate once @jun325 has a major new feature here on github to see if it warrants a bump of the minor or major version (i.e. if it's going to be 2.1.0 or 3.0.0 - suspect that unless we completely redo aViewer, we're mostly going to stick with 2.x.x)


this is sample repository


尝试了新的SSDT-XHC，但是依旧不识别摄像头，不清楚问题所在。
我用SSDT-TB就可以识别。你对比一下看看，是不是XPS13和XPS15的端口差别很大？

![jietu20170312-192201 2x](https://cloud.githubusercontent.com/assets/13273955/23831306/6a65026c-0759-11e7-8da1-0097daee0ff7.jpg)

[SSDT-TB.aml.zip](https://github.com/syscl/XPS9350-macOS/files/836465/SSDT-TB.aml.zip)


Ha ?
Moi m'en suis servi pour un prb d'accent...
Bon du coup je retire ma modif.


уу


![](https://github.trello.services/images/mini-trello-icon.png) [새 기능 추가](https://trello.com/c/Vc1xLNXv/9--)


Давай php будет уюзать только при первом <? в файле, да и то не обязательно.


atribut "lokasi" belum dimasukin ke dlm class gudang


Ah. the backslash should have been removed aswell, sorry. In any case we had double spaces. The space in the sed is not needed!


Shame this line has a diff.


I think adding `eol=lf` will do the trick.


I had a bad experience with submodules few years back but that's probably just because I don't really know how to use them properly. After reading that article I think I might give it a shot. thx


The query parameters are already in context wondering why you need to add them again.


with double spaces ``tr`` will add additional emty lines...


Можно использовать `each.with_index(1)`, чтоб не перебирать индексы вручную (в том числе единичку прибавлять не надо).
А еще на досуге глянь метод [reduce](http://devdocs.io/ruby~2.4/enumerable#method-i-reduce) и попробуй применить его (это не обязательно, но будет полезно).


Peli jonka tein kouluprojektina yksin, jonkun verran koodia katsoin tutoriaaleista ja kaikki 3d-hahmot ja objektit sekä äänet on netistä ladattuja.


ah I see. good like that.


Adds an additional Min/Max check.  These are not solid, but due to the huge XP from a survival loss, (0-280 XP), virtually all legit players will fall in this realm.  I'm being fairly safe with the limits, as high XP players will get lots of bonus XP, though since the max XP is 600k, it's unlikely any will break the system.


Все же удобнее хранить данные в строках, чтоб не приводить к символу при переборе


What does `==` do on TruffleObject? It would make most sense to be able to override that.


`if (`


haha, no changes at all xD


Не в ту степь ушел. Нам требуется перебрать английский алфавит, записать в хэш гласные буквы с индексом в качестве ключа. А ты просто перебрал все гласные буквы (т.е. у гласной буквы `e` должен быть индекс 5, а у тебя будет 2).


음 괜찮은데요?


@amigalemming how does it look [with a custom prelude](https://github.com/lspitzner/pqueue/commit/2175893b04043b2783cc71c4ddb254bd89f744a5)? On the one hand this seems like a future-proof approach to any imports-from-different-base-versions issue; on the other hand it creates more work for people that want to add new code (this Prelude is really minimal); also I am not sure if non-ghc-compilers support `NoImplicitPrelude`.


Oh, it is awesome if the creator still works on his plugin. No?


I have written prelude-compat for this purpose and I am happy if someone uses it.
http://hackage.haskell.org/package/prelude-compat


Wow nice work ! 👍


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/e2e72e06-1684-495f-942f-54308aedf52e "watson-trainer-toolchain"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/244c5b7d-6b8b-4e8b-8719-0e6e1fb7a931 "watson-trainer-toolchain") deployed this commit to [demo01_dev](https://console.ng.bluemix.net/apps/d9c2d969-637b-4929-be9a-a1fc98265465 "ibm:yp:us-south:philippe_mulet@fr.ibm.com:demo01_dev")


The PaginationService's `defaultId` is now a function, so change them to `defaultId()`.


There are many plugins 2 years old on GitHub and they could be very good. I am happy that he made Auth plugin like this. I think it is the best Auth plugin ever.


What did you do man ? I did not get it. Please help me ...


[improvement]

This new option keeps the request open until manually closed with `.end()`. Without this option, the request is automatically closed with `setImmediate`.

This is helpful when working with long lasting connections and with streams.

Example usage:

```js
var stream = request.post({
  url: 'http://...',
  endRequest: false
}, function(err, res, body) {})

stream.write('data')
stream.end()
```


Explain?!


This version fixes the default comment style not working with private messages.


I found the real problem.
It seems, that those globals are never set when an application is backgrounded, but I did add some debugging log messages to elogind itself. And even with debug log messages disabled, the invocation needs those globals to be set right away.
So this was entirely my fault. ;-)


import


yayy


Está mal


[improvement]

This new option reads the response body even if no callback was provided. When set to true, the body will be processed in the same way as it would be with a callback and the body will be passed to the `complete` event.

Helpful when working with streams and expected response is a JSON object. Without this option, the body must be processed and parsed manually.

Example usage:

```js
var stream = request.post({
  url: 'http://...',
  json: true,
  forceReadResponseBody: true
})

stream.on('complete', function(res, body) {
  // body is a JSON object (parsed)
})
```


Так оно не сбилдилось и столько времени просто висело грузом ![d0b9b7.png](https://files.everypony.ru/smiles/3a/f7/d0b9b7.png)
#орхиверниаватаркичтобыможнобыловыкатитьновыйтабунитакиекакянезасиралирепозиторий


@markburns this ends adding a dir without matches, so seems a case for another test. As plugin is for files add a functionality for show dirs seems wrong idea


看到了


Это иллюстрация к тому, как важно правильно называть переменные и аргуемнты


On XenServer 7.0, VM can not start after applying this fix. #34


Actually, this is being used to remove them when `raw-http: true`.


@natugle, thanks


Unless you think we should keep them around.


А зачем вообще перебор? У тебя метод delete вернет nil, если ничего не удалит, либо объект, если удалил. Так и можно проверить, удалился поезд или нет


`@current_station`, не нужно сокращать


Просто сделай 2 метода: один для движения вперед, другой - назад


Only test


Shit


ugh... annoying little program... do as it wants rather than what it's told...AGAIN


What do you think about this? We can't really avoid having two fields being set with the same without casting one to the other. To me, this is the cleanest solution in case we want to extend the plugin later on. Maybe ranks of a specific faction can have a power boost.


Hello,

I'm also working with this package and I'm experiencing an error when creating a cart (getting an internal error from Amazon.) I was looking through forks of the repository and saw your change, and wondered if it's related. May I ask what this change is for?


Would not it be necessary to add it to the default?


i see - it's confusing to call it withQuery but it's to remove the enclosed ones - wihtoutQuery would've made more sense. (I hadn't looked at the rest of the code.)


I think it would be better to make this a `final boolean` field of the node, and have a CExt node that just instantiate it with `callInherited` false. Or alternatively extract the common logic to another node.
Exposing this to Ruby code is really not ideal.


Yes. I'll put it on a todo list to go back and fix.


啊


The "..." commenting strategy applies here as well. Please use

// For each player ...

// ... that is a living player ...

And so forth


Я скорее жду записку и листы/презенташку


should be (true, ...) since there are no parameters, you can skip the check entirely.


Mmmm


This empty line is not needed imo.


The worst thing you could do


I ran test.x 100 times on cab and never encountered the malloc issue.

Recompiling on my mac and rerunning 100 times, I never encountered the malloc issue.  Very weird.


Действительно, не подумал об этом =( Спасибо


Maybe we should change the name of this parameter to psChunk. This way, we could call the later "withChunkX" simply "psChunkX".

We would stick better to our naming scheme and create easier to read code on the way.


- can use 2 command in `sed` and not `tr`
- can exit quotes for not use back slah

     echo "linux pacman KERNEL-core" | sed -e "s/KERNEL/"linux41"/g" -e "s|[[:space:]]|\n|g"


Shouldn't this be `getPort(next)`?


Correct. It was my mistake and have already committed to GitHub before I noticed.


Try to avoid multi layer conditions and keep it as flat, combine these two~


You can throw an error here instead of a log


ок, поправил


Я так назвал чтобы переменная отличалась от имени метода возвращающего текущую станцию.
Изменив на название current_station может мне данную переменную тогда записать в attr_accessor?


We can rename this to Mov?


``[[:space:]]`` is cool! Didn't know that.
In any case @Chrysostomus has already fixed it [properly](https://github.com/Chrysostomus/manjaro-architect/commit/71cb66f117b33691bb7555bb606e1271b3cdea68), nice and simple :wink:


You can use space in test string


![](https://github.trello.services/images/mini-trello-icon.png) [Üst menü search butonun aktif hale getirilmesi](https://trello.com/c/lgUXWV5m/37-ust-menu-search-butonun-aktif-hale-getirilmesi)


Хорошо, понял.


haha


I typically program in Android, which uses jCenter by default. I've heard jCenter has a faster CDN for certain places, and since it's a superset of the Maven Central, I figured "Why not?".


added search and kanban view


Sed/awk is really amazing. There are so many ways of doing the same thing...


This commit makes the shell command `cargo version` panic.


- [ ] vérifier le code
- [ ] vérifier les commentaire


The project is  writen by python flask


Thanks your comment.

Basically, this plugin provides PlantUML image by the commit 24ff58b56a45.
For example, the below plantuml source on URL /owner/repo/**raw**/source.pu. Users can get a rendered image of plantuml source /owner/repo/**plantuml**/source.pu
In addition, users can embedding plantuml in markdonw documents with `![blah](http://[host of gitbucket]/root/repository/plantuml/master/sequence.pu)`


just do a test


可以


对


如果去掉就不能承上启下了


clean formating plz xD


Where should we link to. Gamepedia?


![](https://github.trello.services/images/mini-trello-icon.png) [Ana ekran componentlerinin yerleştirilmesi](https://trello.com/c/msFVRmOB/10-ana-ekran-componentlerinin-yerlestirilmesi)


In a set there are no dupes. That was the idea.


s/partir/partie
@LaurentClaessens


they are mixed values :) snapdragon 820 SCHED eas values come from this table:
https://github.com/Alucard24/Alucard-Kernel-LG-G5/commit/38d25647a904429e73e48ffc05a6b1f950425dc4

I added cluster power from Snapdragon 821 :)


s/conséquences/conséquence
@LaurentClaessens


Why not Type instead of Kind for consistency?

https://github.com/bp74/StageXL/search?utf8=%E2%9C%93&q=type


Didn't you forget the SCSS for the loader, did you?


Yes, that's why the TODO marker at the end. We need to write up general terms too, like what is a style etc.


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/8312b8af-d911-46c8-b967-1d94e7f544be "bluemixlinebotjava"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/355e6327-8e15-4600-9129-5a4556a701c5 "bluemixlinebotjava") deployed this commit to [DicodingClass](https://console.ng.bluemix.net/apps/75183ab3-be7d-4df1-994e-4c44bb67ee0b "ibm:yp:us-south:Lintasarta.PaaS:DicodingClass")


Maybe we should even move it over to the tutorial as a snippet..


@F4z dzięki


Arf, je viens de voir la correction quelques commmits plus loin, désolé  !


@jwt-sgg what do you think? Same for GraphicsPatternKind/Type


Bahnhof. Or is your reaction because of "update process"


Array is clearer than table. Agree on the second part.


Same as above.


Actually this didn't work.  But I think multiple options for mode restriction would be helpful


first comment


test comment


![](https://github.trello.services/images/mini-trello-icon.png) [[등록] 날짜/시간 형식 변경 공통 함수 개발](https://trello.com/c/EZwXHVS9/2--)


@m-kuhn better use links fromthe Devs doc at  http://docs.qgis.org/testing/en/docs/developers_guide/index.html
when 2.8 is released, we'll remove the chapter from qgis.org


same


Related to issue #3


Sure, could you make a pull request (I guess you are faster than me to find the proper location :) )


single space oversight got corrected in next commit


Spokojnie Konrad, pisałem to 3 godziny, security to jest mockup do zmiany
totalnie, zero javadoców, błedy i niedojebane rzeczy są wszędzie, ale nie
jestem czarodziejem, który zrobi doskonale wszystko w 3 h :D Wrzuciłem coś
co działa przyzwoicie, teraz muszę to wszystko poprawić. Zawsze sobie robię
mockupy żeby potem nie zapomnieć że miałem coś zaimplementować :) Nie
spinaj się tak bardzo tym backendem, jest tam w chuj do poprawy ;)

On Sat, Mar 11, 2017 at 11:28 PM, Konrad Tyma <notifications@github.com>
wrote:

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Moi je laisserais le pluriel parce que si il y en avait eu, il y en aurait eu plusieurs.

http://www.academie-francaise.fr/questions-de-langue
section : Aucun / Aucuns

Mais j'avoue que j'aurais du mal à écrire «... n'a aucunes conséquences sur l'ordre ...»


I needed to split this and other type annotations into multiple lines because style-check was complaining about too long lines such as this one and others after the added type for "env"


xDDD Spoko luz, a to nie jest Mateusza commit? Czy ja coś odjebaem xD. ?


nice! att slänga 70 rader utkommenderad kod är alltid snyggt!


@sbeaver-netgate @jim-p @rbgarga  I was on my 2.3.3-p1 Alix and was modifying the items on the System Information Widget. I tried to click the "All" button and wondered why it did not work.
This fix did not get back-ported to RELENG_2_3 RELENG_2_3_3


增加


Bo generalnie my to narazie w commitujemy jak już dorobię te maile + encoder, wieczorem moze napisze kontroler do obslugi tego, tylko przegladam Mateuszowi kod, bo na branchu wspolnym cisniemy. Jak założę Pull requesta, to pewnie bedziemy cos zmieniac ;)