動かなくなりましたという修正依頼の大半がセレクタの書き換えだけで済むものだった気がするので、その場合はコードの変更せず設定変更のみで済むようにしてみた。


I'd add `python2-pip` as `BuildRequires` too...


Fixed with 797e5f8187dfa094e367c09726e1c1c32510c1ed and 39f06597941d8ee669cb81ba172fd23bb521cc06


Good point, I think the value `custom.` is a typo here, it should be `jdbc.ext.` to match the comment above. The exact name is not that important, what's important is that the name can be used in `portal-ext.properties` to define JDBC properties like these:

    jdbc.ext.driverClassName=org.mariadb.jdbc.Driver
    jdbc.ext.url=...
    jdbc.ext.username=...
    jdbc.ext.password=...

Thanks for pointing this out, I'll update this branch accordingly!


зачем тебе переменные `@start_station` и  `@end_station` ? Ты их нигде больше не используешь. Просто сразу добавляй аргументы в массив


Why not using get_formview_action ?


Why is this commented out? How is it destroyed then?


> The rules are very useful to the office extension. I would like to set default to 'on' for LO/OO.
Is it possible in LT?

Not without hard-coding it I think. But I wouldn't even have an issue with that.


We shall need to cut the function from get_datapoints that we can use with custom API, let this function be named _get_datapoints, it shoukd return csv or json or raise error. It is part of code that is below output format=


You've enumerated the pieces, stop using their int representations. It's confusing and unncessary.


Is this valiases or virtualAliases?


fewfwefsdfewf


[R/deprecated.R:17:5:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/deprecated.R#L17) *warning:* **no visible global function definition for ‘prepareRNASeqTemplate’**
```r
    prepareRNASeqTemplate(...)
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/deprecated.R:24:5:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/deprecated.R#L24) *warning:* **no visible global function definition for ‘plotGeneSaturation’**
```r
    plotGeneSaturation(...)
    ^~~~~~~~~~~~~~~~~~
```
[R/deprecated.R:31:5:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/deprecated.R#L31) *warning:* **no visible global function definition for ‘plotDispEsts’**
```r
    plotDispEsts(...)
    ^~~~~~~~~~~~
```
[R/deprecated.R:41:5:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/deprecated.R#L41) *warning:* **no visible global function definition for ‘loadRNASeq’**
```r
    loadRNASeq(...)
    ^~~~~~~~~~
```
[R/internal-tx2gene.R:26:9:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/internal-tx2gene.R#L26) *warning:* **no visible global function definition for ‘tx2gene’**
```r
        tx2gene(organism, release = release)
        ^~~~~~~
```
[R/loadRNASeq.R:62:14:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L62) *warning:* **no visible global function definition for ‘str_match’**
```r
    match <- str_match(projectDir, projectDirPattern)
             ^~~~~~~~~
```
[R/loadRNASeq.R:62:36:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L62) *warning:* **no visible binding for global variable ‘projectDirPattern’**
```r
    match <- str_match(projectDir, projectDirPattern)
                                   ^~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:67:19:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L67) *warning:* **no visible global function definition for ‘.sampleDirs’, Did you mean 'sampleDirs'?**
```r
    sampleDirs <- .sampleDirs(uploadDir)
                  ^~~~~~~~~~~
```
[R/loadRNASeq.R:87:13:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L87) *warning:* **no visible global function definition for ‘readYAML’**
```r
    yaml <- readYAML(yamlFile)
            ^~~~~~~~
```
[R/loadRNASeq.R:96:27:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L96) *warning:* **no visible global function definition for ‘sampleYAMLMetadata’**
```r
        sampleMetadata <- sampleYAMLMetadata(yaml)
                          ^~~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:104:26:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L104) *warning:* **no visible global function definition for ‘camel’, Did you mean 'yaml'?**
```r
    interestingGroups <- camel(interestingGroups, strict = FALSE)
                         ^~~~~
```
[R/loadRNASeq.R:124:17:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L124) *warning:* **no visible global function definition for ‘detectOrganism’**
```r
    organism <- detectOrganism(genomeBuild)
                ^~~~~~~~~~~~~~
```
[R/loadRNASeq.R:136:16:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L136) *warning:* **no visible global function definition for ‘sampleYAMLMetrics’**
```r
    metrics <- sampleYAMLMetrics(yaml)
               ^~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:179:12:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L179) *warning:* **no visible global function definition for ‘.tximport’**
```r
    txi <- .tximport(sampleDirs, tx2gene = tx2gene)
           ^~~~~~~~~
```
[R/loadRNASeq.R:181:12:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L181) *warning:* **no visible global function definition for ‘.tmm’, Did you mean 'tmm'?**
```r
    tmm <- .tmm(rawCounts)
           ^~~~
```
[R/loadRNASeq.R:190:29:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L190) *warning:* **no visible global function definition for ‘DESeq’**
```r
    dds <- suppressWarnings(DESeq(dds))
                            ^~~~~
```
[R/loadRNASeq.R:191:25:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L191) *warning:* **no visible global function definition for ‘counts’, Did you mean 'points'?**
```r
    normalizedCounts <- counts(dds, normalized = TRUE)
                        ^~~~~~
```
[R/loadRNASeq.R:209:16:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L209) *warning:* **no visible global function definition for ‘varianceStabilizingTransformation’**
```r
        vst <- varianceStabilizingTransformation(dds)
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:251:12:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L251) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
    bcb <- new("bcbioRNASeq", se)
           ^~~
```
[R/loadRNASeq.R:253:5:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L253) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
    bcbio(bcb, "tximport") <- txi
    ^~~~~
```
[R/loadRNASeq.R:254:5:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L254) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
    bcbio(bcb, "DESeqDataSet") <- dds
    ^~~~~
```
[R/loadRNASeq.R:257:9:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/loadRNASeq.R#L257) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
        bcbio(bcb, "featureCounts") <- fc
        ^~~~~
```
[R/methods-plotDEGHeatmap.R:64:9:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-plotDEGHeatmap.R#L64) *warning:* **no visible global function definition for ‘plotGeneHeatmap’**
```r
        plotGeneHeatmap(counts, genes = genes, title = title, ...)
        ^~~~~~~~~~~~~~~
```
[R/methods-plotGene.R:65:9:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-plotGene.R#L65) *warning:* **no visible global function definition for ‘show’, Did you mean 'chol'?**
```r
        show(p)
        ^~~~
```
[R/methods-plotGeneHeatmap.R:83:19:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-plotGeneHeatmap.R#L83) *warning:* **no visible global function definition for ‘gene2symbol’**
```r
        counts <- gene2symbol(counts)
                  ^~~~~~~~~~~
```
[R/methods-plotMappingRate.R:51:18:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-plotMappingRate.R#L51) *warning:* **no visible global function definition for ‘qcPassLine’**
```r
        p <- p + qcPassLine(passLimit)
                 ^~~~~~~~~~
```
[R/methods-plotMappingRate.R:54:18:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-plotMappingRate.R#L54) *warning:* **no visible global function definition for ‘qcWarnLine’**
```r
        p <- p + qcWarnLine(warnLimit)
                 ^~~~~~~~~~
```
[R/methods-plotMappingRate.R:57:18:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-plotMappingRate.R#L57) *warning:* **no visible global function definition for ‘coord_flip’**
```r
        p <- p + coord_flip()
                 ^~~~~~~~~~
```
[R/methods-plotPCA.R:45:11:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-plotPCA.R#L45) *warning:* **no visible global function definition for ‘assays’**
```r
    dt <- assays(object)[[transform]]
          ^~~~~~
```
[R/methods-plotPCA.R:65:30:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-plotPCA.R#L65) *warning:* **no visible global function definition for ‘metadata’**
```r
        interestingGroups <- metadata(object)[["interestingGroups"]]
                             ^~~~~~~~
```
[R/methods-plotPCA.R:89:24:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-plotPCA.R#L89) *warning:* **no visible global function definition for ‘colData’**
```r
    data[["label"]] <- colData(object)[, "sampleName"]
                       ^~~~~~~
```
[R/methods-plotPCACovariates.R:60:16:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-plotPCACovariates.R#L60) *warning:* **no visible global function definition for ‘interestingGroups’**
```r
        col <- interestingGroups(object)
               ^~~~~~~~~~~~~~~~~
```
[R/methods-plotVolcano.R:77:14:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-plotVolcano.R#L77) *warning:* **no visible global function definition for ‘left_join’**
```r
    stats <- left_join(stats, g2s, by = "ensgene")
             ^~~~~~~~~
```
[R/methods-resultsTables.R:74:17:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-resultsTables.R#L74) *warning:* **no visible global function definition for ‘.resContrastName’**
```r
    contrast <- .resContrastName(object)
                ^~~~~~~~~~~~~~~~
```
[R/methods-resultsTables.R:75:17:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-resultsTables.R#L75) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
    fileStem <- snake(contrast)
                ^~~~~
```
[R/methods-resultsTables.R:78:14:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-resultsTables.R#L78) *warning:* **no visible global function definition for ‘metadata’**
```r
    alpha <- metadata(object)[["alpha"]]
             ^~~~~~~~
```
[R/methods-resultsTables.R:85:13:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-resultsTables.R#L85) *warning:* **no visible global function definition for ‘annotable’**
```r
    anno <- annotable(genomeBuild)
            ^~~~~~~~~
```
[R/methods-resultsTables.R:142:9:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-resultsTables.R#L142) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(all, file.path(dir, allFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:143:9:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-resultsTables.R#L143) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(deg, file.path(dir, degFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:144:9:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-resultsTables.R#L144) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(degLFCUp, file.path(dir, degLFCUpFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:145:9:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-resultsTables.R#L145) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(degLFCDown, file.path(dir, degLFCDownFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:148:9:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-resultsTables.R#L148) *warning:* **no visible global function definition for ‘.mdResultsTables’**
```r
        .mdResultsTables(resTbl, dir)
        ^~~~~~~~~~~~~~~~
```
[R/methods-resultsTables.R:151:5:](https://github.com/hbc/bcbioRNASeq/blob/a9e3c08047d22706034dec3eaec34ac4f96c400f/R/methods-resultsTables.R#L151) *warning:* **no visible global function definition for ‘mdHeader’**
```r
    mdHeader("Summary statistics", level = headerLevel)
    ^~~~~~~~
```


QTL_power_detect.r has various function to calculate samples size, QTL detection thresholds, and true number of loci given detected QTL for intercross data


И, раз уж править код придётся, лучше переименую переменную `@route`, логичнее список станций хранить в `@stations` или что-то похожее. Тогда не будет странных вызовов, как ниже `@route.route[@count_station]`, будет `@route.stations[@count_station]`


Goby plz


Podać numer konta? Dogadamy się ;)


added files


Creation of the class VectorHelper.


added a file


[R/deprecated.R:17:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/deprecated.R#L17) *warning:* **no visible global function definition for ‘prepareRNASeqTemplate’**
```r
    prepareRNASeqTemplate(...)
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/deprecated.R:24:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/deprecated.R#L24) *warning:* **no visible global function definition for ‘plotGeneSaturation’**
```r
    plotGeneSaturation(...)
    ^~~~~~~~~~~~~~~~~~
```
[R/deprecated.R:31:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/deprecated.R#L31) *warning:* **no visible global function definition for ‘plotDispEsts’**
```r
    plotDispEsts(...)
    ^~~~~~~~~~~~
```
[R/deprecated.R:41:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/deprecated.R#L41) *warning:* **no visible global function definition for ‘loadRNASeq’**
```r
    loadRNASeq(...)
    ^~~~~~~~~~
```
[R/internal-tx2gene.R:26:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/internal-tx2gene.R#L26) *warning:* **no visible global function definition for ‘tx2gene’**
```r
        tx2gene(organism, release = release)
        ^~~~~~~
```
[R/loadRNASeq.R:62:14:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L62) *warning:* **no visible global function definition for ‘str_match’**
```r
    match <- str_match(projectDir, projectDirPattern)
             ^~~~~~~~~
```
[R/loadRNASeq.R:62:36:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L62) *warning:* **no visible binding for global variable ‘projectDirPattern’**
```r
    match <- str_match(projectDir, projectDirPattern)
                                   ^~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:67:19:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L67) *warning:* **no visible global function definition for ‘.sampleDirs’, Did you mean 'sampleDirs'?**
```r
    sampleDirs <- .sampleDirs(uploadDir)
                  ^~~~~~~~~~~
```
[R/loadRNASeq.R:87:13:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L87) *warning:* **no visible global function definition for ‘readYAML’**
```r
    yaml <- readYAML(yamlFile)
            ^~~~~~~~
```
[R/loadRNASeq.R:96:27:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L96) *warning:* **no visible global function definition for ‘sampleYAMLMetadata’**
```r
        sampleMetadata <- sampleYAMLMetadata(yaml)
                          ^~~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:104:26:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L104) *warning:* **no visible global function definition for ‘camel’, Did you mean 'yaml'?**
```r
    interestingGroups <- camel(interestingGroups, strict = FALSE)
                         ^~~~~
```
[R/loadRNASeq.R:124:17:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L124) *warning:* **no visible global function definition for ‘detectOrganism’**
```r
    organism <- detectOrganism(genomeBuild)
                ^~~~~~~~~~~~~~
```
[R/loadRNASeq.R:136:16:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L136) *warning:* **no visible global function definition for ‘sampleYAMLMetrics’**
```r
    metrics <- sampleYAMLMetrics(yaml)
               ^~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:179:12:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L179) *warning:* **no visible global function definition for ‘.tximport’**
```r
    txi <- .tximport(sampleDirs, tx2gene = tx2gene)
           ^~~~~~~~~
```
[R/loadRNASeq.R:181:12:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L181) *warning:* **no visible global function definition for ‘.tmm’, Did you mean 'tmm'?**
```r
    tmm <- .tmm(rawCounts)
           ^~~~
```
[R/loadRNASeq.R:190:29:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L190) *warning:* **no visible global function definition for ‘DESeq’**
```r
    dds <- suppressWarnings(DESeq(dds))
                            ^~~~~
```
[R/loadRNASeq.R:191:25:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L191) *warning:* **no visible global function definition for ‘counts’, Did you mean 'points'?**
```r
    normalizedCounts <- counts(dds, normalized = TRUE)
                        ^~~~~~
```
[R/loadRNASeq.R:209:16:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L209) *warning:* **no visible global function definition for ‘varianceStabilizingTransformation’**
```r
        vst <- varianceStabilizingTransformation(dds)
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:251:12:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L251) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
    bcb <- new("bcbioRNASeq", se)
           ^~~
```
[R/loadRNASeq.R:253:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L253) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
    bcbio(bcb, "tximport") <- txi
    ^~~~~
```
[R/loadRNASeq.R:254:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L254) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
    bcbio(bcb, "DESeqDataSet") <- dds
    ^~~~~
```
[R/loadRNASeq.R:257:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L257) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
        bcbio(bcb, "featureCounts") <- fc
        ^~~~~
```
[R/methods-plotDEGHeatmap.R:64:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotDEGHeatmap.R#L64) *warning:* **no visible global function definition for ‘plotGeneHeatmap’**
```r
        plotGeneHeatmap(counts, genes = genes, title = title, ...)
        ^~~~~~~~~~~~~~~
```
[R/methods-plotGene.R:65:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotGene.R#L65) *warning:* **no visible global function definition for ‘show’, Did you mean 'chol'?**
```r
        show(p)
        ^~~~
```
[R/methods-plotGeneHeatmap.R:83:19:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotGeneHeatmap.R#L83) *warning:* **no visible global function definition for ‘gene2symbol’**
```r
        counts <- gene2symbol(counts)
                  ^~~~~~~~~~~
```
[R/methods-plotMappingRate.R:51:18:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotMappingRate.R#L51) *warning:* **no visible global function definition for ‘qcPassLine’**
```r
        p <- p + qcPassLine(passLimit)
                 ^~~~~~~~~~
```
[R/methods-plotMappingRate.R:54:18:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotMappingRate.R#L54) *warning:* **no visible global function definition for ‘qcWarnLine’**
```r
        p <- p + qcWarnLine(warnLimit)
                 ^~~~~~~~~~
```
[R/methods-plotMappingRate.R:57:18:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotMappingRate.R#L57) *warning:* **no visible global function definition for ‘coord_flip’**
```r
        p <- p + coord_flip()
                 ^~~~~~~~~~
```
[R/methods-plotPCA.R:45:11:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotPCA.R#L45) *warning:* **no visible global function definition for ‘assays’**
```r
    dt <- assays(object)[[transform]]
          ^~~~~~
```
[R/methods-plotPCA.R:65:30:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotPCA.R#L65) *warning:* **no visible global function definition for ‘metadata’**
```r
        interestingGroups <- metadata(object)[["interestingGroups"]]
                             ^~~~~~~~
```
[R/methods-plotPCA.R:89:24:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotPCA.R#L89) *warning:* **no visible global function definition for ‘colData’**
```r
    data[["label"]] <- colData(object)[, "sampleName"]
                       ^~~~~~~
```
[R/methods-plotPCACovariates.R:60:16:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotPCACovariates.R#L60) *warning:* **no visible global function definition for ‘interestingGroups’**
```r
        col <- interestingGroups(object)
               ^~~~~~~~~~~~~~~~~
```
[R/methods-plotVolcano.R:77:14:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotVolcano.R#L77) *warning:* **no visible global function definition for ‘left_join’**
```r
    stats <- left_join(stats, g2s, by = "ensgene")
             ^~~~~~~~~
```
[R/methods-resultsTables.R:74:17:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L74) *warning:* **no visible global function definition for ‘.resContrastName’**
```r
    contrast <- .resContrastName(object)
                ^~~~~~~~~~~~~~~~
```
[R/methods-resultsTables.R:75:17:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L75) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
    fileStem <- snake(contrast)
                ^~~~~
```
[R/methods-resultsTables.R:78:14:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L78) *warning:* **no visible global function definition for ‘metadata’**
```r
    alpha <- metadata(object)[["alpha"]]
             ^~~~~~~~
```
[R/methods-resultsTables.R:85:13:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L85) *warning:* **no visible global function definition for ‘annotable’**
```r
    anno <- annotable(genomeBuild)
            ^~~~~~~~~
```
[R/methods-resultsTables.R:142:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L142) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(all, file.path(dir, allFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:143:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L143) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(deg, file.path(dir, degFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:144:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L144) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(degLFCUp, file.path(dir, degLFCUpFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:145:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L145) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(degLFCDown, file.path(dir, degLFCDownFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:148:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L148) *warning:* **no visible global function definition for ‘.mdResultsTables’**
```r
        .mdResultsTables(resTbl, dir)
        ^~~~~~~~~~~~~~~~
```
[R/methods-resultsTables.R:151:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L151) *warning:* **no visible global function definition for ‘mdHeader’**
```r
    mdHeader("Summary statistics", level = headerLevel)
    ^~~~~~~~
```


Fixes #2


added new file


added this to repo


@josecollazzi I'm assuming if you didn't write this class, we need to include the appropriate license header at the top of the file (if it allows redistribution, that is)


@josecollazzi can you change this to `A driver for the database type "type" could not be found`?


Fixes #3


Помимо изменения индекса станции у поезда необходимо поддерживать актуальным список поездов на станции.
Схема такая: отправили с текущей станции, изменили индекс текущей станции у поезда, на новой текущей станции приняли


hello


@josecollazzi this can probably be an interface instead of an abstract class, using `default` methods for the below implemented methods


замечание аналогично методу next_station


Great news! Althought I was mostly targeting 64-bit platforms, I will see what can we do to make 32-bit code also run faster.


Shame


a) The minimum is clamped to 2. Most interesting cases (close material) are already handled in the existing code which considers pawns == 0 or pawns == 1, and in any case with less than 2 pawns there's no spread so this can't do anything useful.

b + c) I think the combination of knowledge (amount of pawns *and* spread) may be useful and especially handling it via a (drawishness) scale factor rather than a flat bonus. But certainly it's possible that the existing knowledge is good enough.

I thought about using an offset per pawn and an increment per file, but there should probably also be min/max clamps per pawn count, so that's still ~20 parameters.

We'll see if the tuner starts pulling on some of the weights specifically or if it just randomly walks about.


![](https://github.trello.services/images/mini-trello-icon.png) [Implementacao da Preparação de dados.](https://trello.com/c/Qph9IXAW/12-implementacao-da-prepara%C3%A7%C3%A3o-de-dados)


И ещё нужно добавить поезд на станцию, вызвав у объекта станции соответствующий метод.


@josecollazzi this constructor isn't needed :)


![](https://github.trello.services/images/mini-trello-icon.png) [Implementação da Aprendizagem de Máquina na ferramenta.](https://trello.com/c/jnsVDMPR/13-implementa%C3%A7%C3%A3o-da-aprendizagem-de-m%C3%A1quina-na-ferramenta)


did ya test it?


Right, 0x0c definitely makes more sense.


@josecollazzi can you change this to `The database type %s is not supported`?


@MscrmTools Oh, so not all plugins are of ``PluginControlBase`` ?
Sorry about that.


Where is issue ?


布局之间的切换动画


안대에.. 디자인이 추가됬다...크헙
컨텍트 버튼생겨서 좋아졌네요 ㅎ


@marta- Yes, RareConnect will no longer have the patient's name or dob, so this approach unfortunately isn't possible anymore.


Buonasera,
a seguito della sua risposta propongo l'oggetto definitivo da iniziare a modellare trascurando la linea di spirale nella parte superiore.
Attendo conferma
Grazie


:+1: for the "may" :smiley:


[R/deprecated.R:17:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/deprecated.R#L17) *warning:* **no visible global function definition for ‘prepareRNASeqTemplate’**
```r
    prepareRNASeqTemplate(...)
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/deprecated.R:24:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/deprecated.R#L24) *warning:* **no visible global function definition for ‘plotGeneSaturation’**
```r
    plotGeneSaturation(...)
    ^~~~~~~~~~~~~~~~~~
```
[R/deprecated.R:31:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/deprecated.R#L31) *warning:* **no visible global function definition for ‘plotDispEsts’**
```r
    plotDispEsts(...)
    ^~~~~~~~~~~~
```
[R/deprecated.R:41:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/deprecated.R#L41) *warning:* **no visible global function definition for ‘loadRNASeq’**
```r
    loadRNASeq(...)
    ^~~~~~~~~~
```
[R/internal-tx2gene.R:26:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/internal-tx2gene.R#L26) *warning:* **no visible global function definition for ‘tx2gene’**
```r
        tx2gene(organism, release = release)
        ^~~~~~~
```
[R/loadRNASeq.R:62:14:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L62) *warning:* **no visible global function definition for ‘str_match’**
```r
    match <- str_match(projectDir, projectDirPattern)
             ^~~~~~~~~
```
[R/loadRNASeq.R:62:36:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L62) *warning:* **no visible binding for global variable ‘projectDirPattern’**
```r
    match <- str_match(projectDir, projectDirPattern)
                                   ^~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:67:19:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L67) *warning:* **no visible global function definition for ‘.sampleDirs’, Did you mean 'sampleDirs'?**
```r
    sampleDirs <- .sampleDirs(uploadDir)
                  ^~~~~~~~~~~
```
[R/loadRNASeq.R:87:13:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L87) *warning:* **no visible global function definition for ‘readYAML’**
```r
    yaml <- readYAML(yamlFile)
            ^~~~~~~~
```
[R/loadRNASeq.R:96:27:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L96) *warning:* **no visible global function definition for ‘sampleYAMLMetadata’**
```r
        sampleMetadata <- sampleYAMLMetadata(yaml)
                          ^~~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:104:26:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L104) *warning:* **no visible global function definition for ‘camel’, Did you mean 'yaml'?**
```r
    interestingGroups <- camel(interestingGroups, strict = FALSE)
                         ^~~~~
```
[R/loadRNASeq.R:124:17:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L124) *warning:* **no visible global function definition for ‘detectOrganism’**
```r
    organism <- detectOrganism(genomeBuild)
                ^~~~~~~~~~~~~~
```
[R/loadRNASeq.R:136:16:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L136) *warning:* **no visible global function definition for ‘sampleYAMLMetrics’**
```r
    metrics <- sampleYAMLMetrics(yaml)
               ^~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:179:12:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L179) *warning:* **no visible global function definition for ‘.tximport’**
```r
    txi <- .tximport(sampleDirs, tx2gene = tx2gene)
           ^~~~~~~~~
```
[R/loadRNASeq.R:181:12:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L181) *warning:* **no visible global function definition for ‘.tmm’, Did you mean 'tmm'?**
```r
    tmm <- .tmm(rawCounts)
           ^~~~
```
[R/loadRNASeq.R:190:29:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L190) *warning:* **no visible global function definition for ‘DESeq’**
```r
    dds <- suppressWarnings(DESeq(dds))
                            ^~~~~
```
[R/loadRNASeq.R:191:25:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L191) *warning:* **no visible global function definition for ‘counts’, Did you mean 'points'?**
```r
    normalizedCounts <- counts(dds, normalized = TRUE)
                        ^~~~~~
```
[R/loadRNASeq.R:209:16:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L209) *warning:* **no visible global function definition for ‘varianceStabilizingTransformation’**
```r
        vst <- varianceStabilizingTransformation(dds)
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:251:12:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L251) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
    bcb <- new("bcbioRNASeq", se)
           ^~~
```
[R/loadRNASeq.R:253:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L253) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
    bcbio(bcb, "tximport") <- txi
    ^~~~~
```
[R/loadRNASeq.R:254:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L254) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
    bcbio(bcb, "DESeqDataSet") <- dds
    ^~~~~
```
[R/loadRNASeq.R:257:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/loadRNASeq.R#L257) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
        bcbio(bcb, "featureCounts") <- fc
        ^~~~~
```
[R/methods-plotDEGHeatmap.R:64:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotDEGHeatmap.R#L64) *warning:* **no visible global function definition for ‘plotGeneHeatmap’**
```r
        plotGeneHeatmap(counts, genes = genes, title = title, ...)
        ^~~~~~~~~~~~~~~
```
[R/methods-plotGene.R:65:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotGene.R#L65) *warning:* **no visible global function definition for ‘show’, Did you mean 'chol'?**
```r
        show(p)
        ^~~~
```
[R/methods-plotGeneHeatmap.R:83:19:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotGeneHeatmap.R#L83) *warning:* **no visible global function definition for ‘gene2symbol’**
```r
        counts <- gene2symbol(counts)
                  ^~~~~~~~~~~
```
[R/methods-plotMappingRate.R:51:18:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotMappingRate.R#L51) *warning:* **no visible global function definition for ‘qcPassLine’**
```r
        p <- p + qcPassLine(passLimit)
                 ^~~~~~~~~~
```
[R/methods-plotMappingRate.R:54:18:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotMappingRate.R#L54) *warning:* **no visible global function definition for ‘qcWarnLine’**
```r
        p <- p + qcWarnLine(warnLimit)
                 ^~~~~~~~~~
```
[R/methods-plotMappingRate.R:57:18:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotMappingRate.R#L57) *warning:* **no visible global function definition for ‘coord_flip’**
```r
        p <- p + coord_flip()
                 ^~~~~~~~~~
```
[R/methods-plotPCA.R:45:11:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotPCA.R#L45) *warning:* **no visible global function definition for ‘assays’**
```r
    dt <- assays(object)[[transform]]
          ^~~~~~
```
[R/methods-plotPCA.R:65:30:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotPCA.R#L65) *warning:* **no visible global function definition for ‘metadata’**
```r
        interestingGroups <- metadata(object)[["interestingGroups"]]
                             ^~~~~~~~
```
[R/methods-plotPCA.R:89:24:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotPCA.R#L89) *warning:* **no visible global function definition for ‘colData’**
```r
    data[["label"]] <- colData(object)[, "sampleName"]
                       ^~~~~~~
```
[R/methods-plotPCACovariates.R:60:16:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotPCACovariates.R#L60) *warning:* **no visible global function definition for ‘interestingGroups’**
```r
        col <- interestingGroups(object)
               ^~~~~~~~~~~~~~~~~
```
[R/methods-plotVolcano.R:77:14:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-plotVolcano.R#L77) *warning:* **no visible global function definition for ‘left_join’**
```r
    stats <- left_join(stats, g2s, by = "ensgene")
             ^~~~~~~~~
```
[R/methods-resultsTables.R:74:17:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L74) *warning:* **no visible global function definition for ‘.resContrastName’**
```r
    contrast <- .resContrastName(object)
                ^~~~~~~~~~~~~~~~
```
[R/methods-resultsTables.R:75:17:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L75) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
    fileStem <- snake(contrast)
                ^~~~~
```
[R/methods-resultsTables.R:78:14:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L78) *warning:* **no visible global function definition for ‘metadata’**
```r
    alpha <- metadata(object)[["alpha"]]
             ^~~~~~~~
```
[R/methods-resultsTables.R:85:13:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L85) *warning:* **no visible global function definition for ‘annotable’**
```r
    anno <- annotable(genomeBuild)
            ^~~~~~~~~
```
[R/methods-resultsTables.R:142:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L142) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(all, file.path(dir, allFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:143:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L143) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(deg, file.path(dir, degFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:144:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L144) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(degLFCUp, file.path(dir, degLFCUpFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:145:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L145) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(degLFCDown, file.path(dir, degLFCDownFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:148:9:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L148) *warning:* **no visible global function definition for ‘.mdResultsTables’**
```r
        .mdResultsTables(resTbl, dir)
        ^~~~~~~~~~~~~~~~
```
[R/methods-resultsTables.R:151:5:](https://github.com/hbc/bcbioRNASeq/blob/aa3fa55cd697851a281d2e3350209505c8f2244f/R/methods-resultsTables.R#L151) *warning:* **no visible global function definition for ‘mdHeader’**
```r
    mdHeader("Summary statistics", level = headerLevel)
    ^~~~~~~~
```


Fix for Issue #3


I wish I was surprised that this exists but I'm really not, @ibnesayeed ;)


update


OK, I give up. I'll use the linter and make the necessary corrections.


Bluemix [toolchain](https://console.bluemix.net/devops/toolchains/054cbe60-4caf-4379-836b-6a81f1190963 "simple-toolchain-jspv1"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/5a3bf57d-9c72-4269-800c-bb43de795574 "simple-toolchain-jspv1") deployed [simple-toolchain-jspv1](https://github.com/jesiels/simple-toolchain-jspv1/releases/tag/deploy-ibm-yp-us-south-jesiels-br.ibm.com-dev-20171017-151027 "deploy-ibm-yp-us-south-jesiels-br.ibm.com-dev-20171017-151027") to [dev](https://console.bluemix.net/apps/8b17bc39-6d5f-4f4c-afa6-835716248529?env_id=ibm:yp:us-south "ibm:yp:us-south:jesiels@br.ibm.com:dev"), including this commit


Может, стоит осуществлять преобразование q_title -> q_uri в JS, тогда избавимся от зависимости в этом расширении Parsedown. Но придется синхронизировать паттерны замены PHP <-> JS


hmm, þetta virðist ekki hafa virkað, kanna málið


Also did a bit of refactoring here and moved appointments to a 'pack'


m.me/naymaakter.joya


Здесь тоже стоит добавить валидации: проверять, что переданы именно объекты станций


google map style does not work on my computer can you try on yours.


IMHO using === here  is to risky...


Bluemix [toolchain](https://console.bluemix.net/devops/toolchains/6146f495-28a9-4f42-a712-da2e87b9975d "blg361"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/4a604f6d-2b15-4773-8e37-c880f9ba00aa "itucsdb1701") deployed [itucsdb1701](https://github.com/itucsdb1701/itucsdb1701/releases/tag/deploy-ibm-yp-us-south-itucsdb17-BLG361-20171017-151157 "deploy-ibm-yp-us-south-itucsdb17-BLG361-20171017-151157") to [BLG361](https://console.bluemix.net/apps/772da3c3-d162-4407-820f-35f3cbb651d6?env_id=ibm:yp:us-south "ibm:yp:us-south:itucsdb17:BLG361"), including this commit


Haha, thank you 🎩


IMHO using === here is too risky...


CLM-294 start
CLM-295 start
CLM-293 start


@jn0 would you mind creating a quick PR to add that please?


OK. I will try


retona fase anterior


Do you need to add a line setting first to false after the first time through the loop?


This isn't correct; it produces silliness like the following,
```
install -m 755 ./ed "/nix/store/qw21f11wssyfyfif70nw3psbmwm966zj-ed-1.14.2x86_64-unknown-linux-gnu-/bin/ed"
```


[R/deprecated.R:17:5:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/deprecated.R#L17) *warning:* **no visible global function definition for ‘prepareRNASeqTemplate’**
```r
    prepareRNASeqTemplate(...)
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/deprecated.R:24:5:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/deprecated.R#L24) *warning:* **no visible global function definition for ‘plotGeneSaturation’**
```r
    plotGeneSaturation(...)
    ^~~~~~~~~~~~~~~~~~
```
[R/deprecated.R:31:5:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/deprecated.R#L31) *warning:* **no visible global function definition for ‘plotDispEsts’**
```r
    plotDispEsts(...)
    ^~~~~~~~~~~~
```
[R/deprecated.R:41:5:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/deprecated.R#L41) *warning:* **no visible global function definition for ‘loadRNASeq’**
```r
    loadRNASeq(...)
    ^~~~~~~~~~
```
[R/internal-tx2gene.R:26:9:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/internal-tx2gene.R#L26) *warning:* **no visible global function definition for ‘tx2gene’**
```r
        tx2gene(organism, release = release)
        ^~~~~~~
```
[R/loadRNASeq.R:62:14:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L62) *warning:* **no visible global function definition for ‘str_match’**
```r
    match <- str_match(projectDir, projectDirPattern)
             ^~~~~~~~~
```
[R/loadRNASeq.R:62:36:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L62) *warning:* **no visible binding for global variable ‘projectDirPattern’**
```r
    match <- str_match(projectDir, projectDirPattern)
                                   ^~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:67:19:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L67) *warning:* **no visible global function definition for ‘.sampleDirs’, Did you mean 'sampleDirs'?**
```r
    sampleDirs <- .sampleDirs(uploadDir)
                  ^~~~~~~~~~~
```
[R/loadRNASeq.R:87:13:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L87) *warning:* **no visible global function definition for ‘readYAML’**
```r
    yaml <- readYAML(yamlFile)
            ^~~~~~~~
```
[R/loadRNASeq.R:96:27:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L96) *warning:* **no visible global function definition for ‘sampleYAMLMetadata’**
```r
        sampleMetadata <- sampleYAMLMetadata(yaml)
                          ^~~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:104:26:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L104) *warning:* **no visible global function definition for ‘camel’, Did you mean 'yaml'?**
```r
    interestingGroups <- camel(interestingGroups, strict = FALSE)
                         ^~~~~
```
[R/loadRNASeq.R:124:17:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L124) *warning:* **no visible global function definition for ‘detectOrganism’**
```r
    organism <- detectOrganism(genomeBuild)
                ^~~~~~~~~~~~~~
```
[R/loadRNASeq.R:136:16:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L136) *warning:* **no visible global function definition for ‘sampleYAMLMetrics’**
```r
    metrics <- sampleYAMLMetrics(yaml)
               ^~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:179:12:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L179) *warning:* **no visible global function definition for ‘.tximport’**
```r
    txi <- .tximport(sampleDirs, tx2gene = tx2gene)
           ^~~~~~~~~
```
[R/loadRNASeq.R:181:12:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L181) *warning:* **no visible global function definition for ‘.tmm’, Did you mean 'tmm'?**
```r
    tmm <- .tmm(rawCounts)
           ^~~~
```
[R/loadRNASeq.R:190:29:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L190) *warning:* **no visible global function definition for ‘DESeq’**
```r
    dds <- suppressWarnings(DESeq(dds))
                            ^~~~~
```
[R/loadRNASeq.R:191:25:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L191) *warning:* **no visible global function definition for ‘counts’, Did you mean 'points'?**
```r
    normalizedCounts <- counts(dds, normalized = TRUE)
                        ^~~~~~
```
[R/loadRNASeq.R:209:16:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L209) *warning:* **no visible global function definition for ‘varianceStabilizingTransformation’**
```r
        vst <- varianceStabilizingTransformation(dds)
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/loadRNASeq.R:251:12:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L251) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
    bcb <- new("bcbioRNASeq", se)
           ^~~
```
[R/loadRNASeq.R:253:5:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L253) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
    bcbio(bcb, "tximport") <- txi
    ^~~~~
```
[R/loadRNASeq.R:254:5:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L254) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
    bcbio(bcb, "DESeqDataSet") <- dds
    ^~~~~
```
[R/loadRNASeq.R:257:9:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/loadRNASeq.R#L257) *warning:* **no visible global function definition for ‘bcbio<-’**
```r
        bcbio(bcb, "featureCounts") <- fc
        ^~~~~
```
[R/methods-plotDEGHeatmap.R:64:9:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-plotDEGHeatmap.R#L64) *warning:* **no visible global function definition for ‘plotGeneHeatmap’**
```r
        plotGeneHeatmap(counts, genes = genes, title = title, ...)
        ^~~~~~~~~~~~~~~
```
[R/methods-plotGene.R:65:9:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-plotGene.R#L65) *warning:* **no visible global function definition for ‘show’, Did you mean 'chol'?**
```r
        show(p)
        ^~~~
```
[R/methods-plotGeneHeatmap.R:83:19:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-plotGeneHeatmap.R#L83) *warning:* **no visible global function definition for ‘gene2symbol’**
```r
        counts <- gene2symbol(counts)
                  ^~~~~~~~~~~
```
[R/methods-plotMappingRate.R:51:18:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-plotMappingRate.R#L51) *warning:* **no visible global function definition for ‘qcPassLine’**
```r
        p <- p + qcPassLine(passLimit)
                 ^~~~~~~~~~
```
[R/methods-plotMappingRate.R:54:18:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-plotMappingRate.R#L54) *warning:* **no visible global function definition for ‘qcWarnLine’**
```r
        p <- p + qcWarnLine(warnLimit)
                 ^~~~~~~~~~
```
[R/methods-plotMappingRate.R:57:18:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-plotMappingRate.R#L57) *warning:* **no visible global function definition for ‘coord_flip’**
```r
        p <- p + coord_flip()
                 ^~~~~~~~~~
```
[R/methods-plotPCA.R:45:11:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-plotPCA.R#L45) *warning:* **no visible global function definition for ‘assays’**
```r
    dt <- assays(object)[[transform]]
          ^~~~~~
```
[R/methods-plotPCA.R:65:30:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-plotPCA.R#L65) *warning:* **no visible global function definition for ‘metadata’**
```r
        interestingGroups <- metadata(object)[["interestingGroups"]]
                             ^~~~~~~~
```
[R/methods-plotPCA.R:89:24:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-plotPCA.R#L89) *warning:* **no visible global function definition for ‘colData’**
```r
    data[["label"]] <- colData(object)[, "sampleName"]
                       ^~~~~~~
```
[R/methods-plotPCACovariates.R:60:16:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-plotPCACovariates.R#L60) *warning:* **no visible global function definition for ‘interestingGroups’**
```r
        col <- interestingGroups(object)
               ^~~~~~~~~~~~~~~~~
```
[R/methods-plotVolcano.R:77:14:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-plotVolcano.R#L77) *warning:* **no visible global function definition for ‘left_join’**
```r
    stats <- left_join(stats, g2s, by = "ensgene")
             ^~~~~~~~~
```
[R/methods-resultsTables.R:74:17:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-resultsTables.R#L74) *warning:* **no visible global function definition for ‘.resContrastName’**
```r
    contrast <- .resContrastName(object)
                ^~~~~~~~~~~~~~~~
```
[R/methods-resultsTables.R:75:17:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-resultsTables.R#L75) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
    fileStem <- snake(contrast)
                ^~~~~
```
[R/methods-resultsTables.R:78:14:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-resultsTables.R#L78) *warning:* **no visible global function definition for ‘metadata’**
```r
    alpha <- metadata(object)[["alpha"]]
             ^~~~~~~~
```
[R/methods-resultsTables.R:85:13:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-resultsTables.R#L85) *warning:* **no visible global function definition for ‘annotable’**
```r
    anno <- annotable(genomeBuild)
            ^~~~~~~~~
```
[R/methods-resultsTables.R:142:9:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-resultsTables.R#L142) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(all, file.path(dir, allFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:143:9:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-resultsTables.R#L143) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(deg, file.path(dir, degFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:144:9:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-resultsTables.R#L144) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(degLFCUp, file.path(dir, degLFCUpFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:145:9:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-resultsTables.R#L145) *warning:* **no visible global function definition for ‘write_csv’, Did you mean 'write.csv'?**
```r
        write_csv(degLFCDown, file.path(dir, degLFCDownFile))
        ^~~~~~~~~
```
[R/methods-resultsTables.R:148:9:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-resultsTables.R#L148) *warning:* **no visible global function definition for ‘.mdResultsTables’**
```r
        .mdResultsTables(resTbl, dir)
        ^~~~~~~~~~~~~~~~
```
[R/methods-resultsTables.R:151:5:](https://github.com/hbc/bcbioRNASeq/blob/a5feaff144e29b131d7016e89298a0f9810f7b40/R/methods-resultsTables.R#L151) *warning:* **no visible global function definition for ‘mdHeader’**
```r
    mdHeader("Summary statistics", level = headerLevel)
    ^~~~~~~~
```


Pinging @Ericson2314.


Hey, thanks for doing this! Looks really good! Right now we have everything we need to display actions and their payload (and the current state, not sure if thats helpful). Since actions can be async I'm not sure if we could do a mapping of actions -> mutations, if you have an idea I would love to hear it.

What about if we start by just displaying what we have? List of actions, that you can inspect the time, type, payload.


de


Needs to be in a single transaction


The following doc(s) have been deployed to the [2139drumme](https://2139drumme-static-docs.pantheonsite.io/docs) Multidev environment:
- [/docs/guides/drupal-8-commerce](https://2139drumme-static-docs.pantheonsite.io/docs/guides/drupal-8-commerce)
- [source/docs/assets/images/guides/drupal-8-commerce/install-modules.png](https://github.com/pantheon-systems/documentation/commit/4e29eb45d9171585f99e03aebe181a460a68dd2f/source/docs/assets/images/guides/drupal-8-commerce/install-modules.png)
- [source/docs/assets/images/guides/drupal-8-commerce/visit-dev-site.png](https://github.com/pantheon-systems/documentation/commit/4e29eb45d9171585f99e03aebe181a460a68dd2f/source/docs/assets/images/guides/drupal-8-commerce/visit-dev-site.png)


Minor: less redundant approach `woopra.identify(client.match(/^(id|id-dev)\.onfido\.com$/) ? {sdk_version} : {sdk_version, client})`


Może załatwimy to poza "systemem" - zapłacę w naturze - szyszkami  - może być? - daję 3 szyszki za każą literówkę (na dobry początek). W razie pytań: szyszki sosnowe, oryginalne, sosna pochodzi z mojego ogródka, zbieram osobiście.


this would benefit from a comment, since it's not immediately obvious why this is happening.


Why is this needed?


Good job. Please, explain the function of each line. You can add comment line to explain.


woo


Bluemix [toolchain](https://console.bluemix.net/devops/toolchains/6146f495-28a9-4f42-a712-da2e87b9975d "blg361"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/4a604f6d-2b15-4773-8e37-c880f9ba00aa "itucsdb1701") deployed [itucsdb1701](https://github.com/itucsdb1701/itucsdb1701/releases/tag/deploy-ibm-yp-us-south-itucsdb17-BLG361-20171017-151755 "deploy-ibm-yp-us-south-itucsdb17-BLG361-20171017-151755") to [BLG361](https://console.bluemix.net/apps/772da3c3-d162-4407-820f-35f3cbb651d6?env_id=ibm:yp:us-south "ibm:yp:us-south:itucsdb17:BLG361"), including this commit


wow that's great!


https://www.programiz.com/c-programming/examples/factorial
looks like copied


No, leave it in. I believe Ryan is going to be adding the same change to the rest of our repos.


This should probably be `... = ex` now that I look at it again.


ah, so `an_mlv_cache_thread` is the problem. Well I guess that's what it would be. Weirddd :(

Wasn't it more stable at some earlier point? I have a feeling that one of the more recent commits made caching more unstable, or no one noticed it at first.

Anyway, I'll be able to do LOADS next week(free time is going to appear). White balance picker up next, that's really overdue :)


No need for async/await - same for the following functions


No, it necessary. O.W, when i = 0, executing i-1 will also make (i >= 0) true.


commento


I am getting an error here where it says getUserByUsername is not a function


OK, I'll shorter the lines.

> These lines, when formatted with the two indents, are 83 characters long,

Did you mean 84? These lines are 72 columns wide, and I guess indentation would add 4, 8, or 12 lines, not an odd number such as 11.

Either way, removing the space around the `+` operators should suffice.


I think it is enough if we name it "Reset", cause you have information in the description what actually it is doing.


ciao


no problem...

Plugins that need two connections cannot inherit from `PluginControlBase` because they need to get more than one service


each is preferred, map is for using the returned value.


Remove the only


This breaks desktop integration as it will always return an empty string!
It would be better to check this with `[ -x "$(command -v $DEP)" ]`


You created this call just for testing, but you could've used the existing API call that returns all the questions, and check that the one you deleted isn't there.


FF56 on W7 says
```
XML Parsing Error: unclosed token
Location: data:image/svg+xml,%3Csvg%20xmlns='http://www.w3.org/2000/svg'%20width='16'%20height='16'%20viewBox='0%200%2016%2016'%3E%3Cpath%20fill='#333333'%20d='M14%208L9%203v3H2v4h7v3z'/%3E%3C/svg%3E
Line Number 1, Column 84:

<svg xmlns='http://www.w3.org/2000/svg' width='16' height='16' viewBox='0 0 16 16'><path fill='
-----------------------------------------------------------------------------------^
```
and no navigation arrows/spinner are displayed.


You should remove `~sync:true`, as the sync message has already been sent.


@jonjomckay I have got the class from this example https://github.com/Microsoft/mssql-jdbc/wiki/Custom-TrustManager it seems official docs, should I add something to the code about that?


The following doc(s) have been deployed to the [2139drumme](https://2139drumme-static-docs.pantheonsite.io/docs) Multidev environment:
- [/docs/guides/drupal-8-commerce](https://2139drumme-static-docs.pantheonsite.io/docs/guides/drupal-8-commerce)
- [source/docs/assets/images/guides/drupal-8-commerce/install-modules.png](https://github.com/pantheon-systems/documentation/commit/4e29eb45d9171585f99e03aebe181a460a68dd2f/source/docs/assets/images/guides/drupal-8-commerce/install-modules.png)
- [source/docs/assets/images/guides/drupal-8-commerce/visit-dev-site.png](https://github.com/pantheon-systems/documentation/commit/4e29eb45d9171585f99e03aebe181a460a68dd2f/source/docs/assets/images/guides/drupal-8-commerce/visit-dev-site.png)


You've added more mistakes than fixed ;)


@optilude Jenkins CI reporting about code analysis
See the full report here: http://jenkins.plone.org/job/package-borg.localrole/1/violations
```
borg/__init__.py:0:1: C101 Coding magic comment not found
borg/localrole/config.py:0:1: C101 Coding magic comment not found
borg/localrole/config.py:3:42: W292 no newline at end of file
borg/localrole/tests.py:0:1: C101 Coding magic comment not found
borg/localrole/tests.py:1:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:2:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:3:1: I004 isort found an unexpected blank line in imports
borg/localrole/tests.py:4:1: F401 'zope.testing.doctestunit' imported but unused
borg/localrole/tests.py:4:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:5:1: F401 'zope.component.testing' imported but unused
borg/localrole/tests.py:5:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:6:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:7:1: I004 isort found an unexpected blank line in imports
borg/localrole/tests.py:9:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:10:1: I004 isort found an unexpected blank line in imports
borg/localrole/tests.py:15:1: I003 isort expected 1 blank line in imports, found 0
borg/localrole/tests.py:18:1: E302 expected 2 blank lines, found 1
borg/localrole/tests.py:27:1: E302 expected 2 blank lines, found 1
borg/localrole/tests.py:33:44: W291 trailing whitespace
borg/localrole/tests.py:36:1: W293 blank line contains whitespace
borg/localrole/tests.py:39:1: E305 expected 2 blank lines after class or function definition, found 1
borg/localrole/interfaces.py:0:1: C101 Coding magic comment not found
borg/localrole/interfaces.py:2:1: I003 isort expected 1 blank line in imports, found 0
borg/localrole/interfaces.py:3:1: E302 expected 2 blank lines, found 1
borg/localrole/interfaces.py:5:1: W293 blank line contains whitespace
borg/localrole/interfaces.py:6:74: W291 trailing whitespace
borg/localrole/interfaces.py:7:72: W291 trailing whitespace
borg/localrole/interfaces.py:10:1: W293 blank line contains whitespace
borg/localrole/__init__.py:0:1: C101 Coding magic comment not found
borg/localrole/__init__.py:2:1: I001 isort found an import in the wrong position
borg/localrole/__init__.py:4:1: I001 isort found an import in the wrong position
borg/localrole/__init__.py:8:1: E302 expected 2 blank lines, found 1
borg/localrole/__init__.py:11:1: W293 blank line contains whitespace
borg/localrole/__init__.py:13:37: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:13:39: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:14:39: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:14:41: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:14:80: E501 line too long (92 > 79 characters)
borg/localrole/__init__.py:15:80: E501 line too long (89 > 79 characters)
borg/localrole/__init__.py:16:37: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:16:39: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:16:45: W292 no newline at end of file
borg/localrole/utils.py:0:1: C101 Coding magic comment not found
borg/localrole/utils.py:3:1: I001 isort found an import in the wrong position
borg/localrole/utils.py:4:1: I001 isort found an import in the wrong position
borg/localrole/utils.py:5:1: I004 isort found an unexpected blank line in imports
borg/localrole/utils.py:6:1: I001 isort found an import in the wrong position
borg/localrole/utils.py:8:1: E302 expected 2 blank lines, found 1
borg/localrole/utils.py:12:1: W293 blank line contains whitespace
borg/localrole/utils.py:22:9: T001 print statement found.
borg/localrole/utils.py:22:23: Q000 Remove bad quotes.
borg/localrole/utils.py:22:23: S001 found module formatter
borg/localrole/utils.py:23:1: W293 blank line contains whitespace
borg/localrole/utils.py:24:26: W292 no newline at end of file
borg/localrole/workspace.py:0:1: C101 Coding magic comment not found
borg/localrole/workspace.py:7:1: F401 'Acquisition.aq_chain' imported but unused
borg/localrole/workspace.py:7:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:8:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:11:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:12:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:13:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:14:1: I004 isort found an unexpected blank line in imports
borg/localrole/workspace.py:15:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:18:9: Q000 Remove bad quotes.
borg/localrole/workspace.py:19:18: Q000 Remove bad quotes.
borg/localrole/workspace.py:21:1: E302 expected 2 blank lines, found 1
borg/localrole/workspace.py:21:80: E501 line too long (82 > 79 characters)
borg/localrole/workspace.py:22:80: E501 line too long (81 > 79 characters)
borg/localrole/workspace.py:28:17: S001 found module formatter
borg/localrole/workspace.py:28:80: E501 line too long (90 > 79 characters)
borg/localrole/workspace.py:31:1: E302 expected 2 blank lines, found 1
borg/localrole/workspace.py:32:17: Q000 Remove bad quotes.
borg/localrole/workspace.py:33:13: E221 multiple spaces before operator
borg/localrole/workspace.py:43:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:43:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:44:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:51:1: W293 blank line contains whitespace
borg/localrole/workspace.py:54:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:54:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:55:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:57:1: W293 blank line contains whitespace
borg/localrole/workspace.py:66:1: W293 blank line contains whitespace
borg/localrole/workspace.py:69:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:69:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:70:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:72:1: W293 blank line contains whitespace
borg/localrole/workspace.py:78:1: W293 blank line contains whitespace
borg/localrole/workspace.py:80:1: W293 blank line contains whitespace
borg/localrole/workspace.py:82:1: W293 blank line contains whitespace
borg/localrole/workspace.py:83:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:83:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:84:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:89:1: W293 blank line contains whitespace
borg/localrole/workspace.py:95:1: W293 blank line contains whitespace
borg/localrole/workspace.py:96:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:96:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:97:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:98:73: W291 trailing whitespace
borg/localrole/workspace.py:101:1: W293 blank line contains whitespace
borg/localrole/workspace.py:107:75: W291 trailing whitespace
borg/localrole/workspace.py:108:77: W291 trailing whitespace
borg/localrole/workspace.py:112:1: W293 blank line contains whitespace
borg/localrole/workspace.py:115:1: W293 blank line contains whitespace
borg/localrole/workspace.py:116:58: E202 whitespace before ')'
borg/localrole/workspace.py:120:80: E501 line too long (80 > 79 characters)
borg/localrole/workspace.py:121:80: E501 line too long (81 > 79 characters)
borg/localrole/workspace.py:124:1: E305 expected 2 blank lines after class or function definition, found 1
```
Follow [these instructions](https://github.com/plone/jenkins.plone.org/blob/master/docs/source/run-qa-on-package.rst) to reproduce it locally.


@optilude Jenkins CI reporting about code analysis
See the full report here: http://jenkins.plone.org/job/package-borg.localrole/2/violations
```
borg/__init__.py:0:1: C101 Coding magic comment not found
borg/localrole/config.py:0:1: C101 Coding magic comment not found
borg/localrole/config.py:3:42: W292 no newline at end of file
borg/localrole/tests.py:0:1: C101 Coding magic comment not found
borg/localrole/tests.py:1:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:2:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:3:1: I004 isort found an unexpected blank line in imports
borg/localrole/tests.py:4:1: F401 'zope.testing.doctestunit' imported but unused
borg/localrole/tests.py:4:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:5:1: F401 'zope.component.testing' imported but unused
borg/localrole/tests.py:5:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:6:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:7:1: I004 isort found an unexpected blank line in imports
borg/localrole/tests.py:9:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:10:1: I004 isort found an unexpected blank line in imports
borg/localrole/tests.py:15:1: I003 isort expected 1 blank line in imports, found 0
borg/localrole/tests.py:18:1: E302 expected 2 blank lines, found 1
borg/localrole/tests.py:27:1: E302 expected 2 blank lines, found 1
borg/localrole/tests.py:33:44: W291 trailing whitespace
borg/localrole/tests.py:36:1: W293 blank line contains whitespace
borg/localrole/tests.py:39:1: E305 expected 2 blank lines after class or function definition, found 1
borg/localrole/interfaces.py:0:1: C101 Coding magic comment not found
borg/localrole/interfaces.py:2:1: I003 isort expected 1 blank line in imports, found 0
borg/localrole/interfaces.py:3:1: E302 expected 2 blank lines, found 1
borg/localrole/interfaces.py:5:1: W293 blank line contains whitespace
borg/localrole/interfaces.py:6:74: W291 trailing whitespace
borg/localrole/interfaces.py:7:72: W291 trailing whitespace
borg/localrole/interfaces.py:10:1: W293 blank line contains whitespace
borg/localrole/interfaces.py:20:1: E302 expected 2 blank lines, found 1
borg/localrole/interfaces.py:22:1: W293 blank line contains whitespace
borg/localrole/interfaces.py:26:1: W293 blank line contains whitespace
borg/localrole/interfaces.py:30:8: W292 no newline at end of file
borg/localrole/__init__.py:0:1: C101 Coding magic comment not found
borg/localrole/__init__.py:2:1: I001 isort found an import in the wrong position
borg/localrole/__init__.py:4:1: I001 isort found an import in the wrong position
borg/localrole/__init__.py:8:1: E302 expected 2 blank lines, found 1
borg/localrole/__init__.py:11:1: W293 blank line contains whitespace
borg/localrole/__init__.py:13:37: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:13:39: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:14:39: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:14:41: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:14:80: E501 line too long (92 > 79 characters)
borg/localrole/__init__.py:15:80: E501 line too long (89 > 79 characters)
borg/localrole/__init__.py:16:37: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:16:39: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:16:45: W292 no newline at end of file
borg/localrole/utils.py:0:1: C101 Coding magic comment not found
borg/localrole/utils.py:3:1: I001 isort found an import in the wrong position
borg/localrole/utils.py:4:1: I001 isort found an import in the wrong position
borg/localrole/utils.py:5:1: I004 isort found an unexpected blank line in imports
borg/localrole/utils.py:6:1: I001 isort found an import in the wrong position
borg/localrole/utils.py:8:1: E302 expected 2 blank lines, found 1
borg/localrole/utils.py:12:1: W293 blank line contains whitespace
borg/localrole/utils.py:22:9: T001 print statement found.
borg/localrole/utils.py:22:23: Q000 Remove bad quotes.
borg/localrole/utils.py:22:23: S001 found module formatter
borg/localrole/utils.py:23:1: W293 blank line contains whitespace
borg/localrole/utils.py:24:26: W292 no newline at end of file
borg/localrole/workspace.py:0:1: C101 Coding magic comment not found
borg/localrole/workspace.py:7:1: F401 'Acquisition.aq_chain' imported but unused
borg/localrole/workspace.py:7:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:8:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:11:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:12:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:13:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:14:1: I004 isort found an unexpected blank line in imports
borg/localrole/workspace.py:15:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:16:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:19:9: Q000 Remove bad quotes.
borg/localrole/workspace.py:20:18: Q000 Remove bad quotes.
borg/localrole/workspace.py:22:1: E302 expected 2 blank lines, found 1
borg/localrole/workspace.py:22:80: E501 line too long (82 > 79 characters)
borg/localrole/workspace.py:23:80: E501 line too long (81 > 79 characters)
borg/localrole/workspace.py:29:17: S001 found module formatter
borg/localrole/workspace.py:29:80: E501 line too long (90 > 79 characters)
borg/localrole/workspace.py:32:1: E302 expected 2 blank lines, found 1
borg/localrole/workspace.py:33:17: Q000 Remove bad quotes.
borg/localrole/workspace.py:34:13: E221 multiple spaces before operator
borg/localrole/workspace.py:44:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:44:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:45:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:57:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:57:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:58:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:60:1: W293 blank line contains whitespace
borg/localrole/workspace.py:65:1: W293 blank line contains whitespace
borg/localrole/workspace.py:72:1: W293 blank line contains whitespace
borg/localrole/workspace.py:75:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:75:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:76:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:78:1: W293 blank line contains whitespace
borg/localrole/workspace.py:82:1: W293 blank line contains whitespace
borg/localrole/workspace.py:84:1: W293 blank line contains whitespace
borg/localrole/workspace.py:86:1: W293 blank line contains whitespace
borg/localrole/workspace.py:87:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:87:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:88:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:93:1: W293 blank line contains whitespace
borg/localrole/workspace.py:99:1: W293 blank line contains whitespace
borg/localrole/workspace.py:100:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:100:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:101:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:102:73: W291 trailing whitespace
borg/localrole/workspace.py:105:1: W293 blank line contains whitespace
borg/localrole/workspace.py:111:75: W291 trailing whitespace
borg/localrole/workspace.py:112:77: W291 trailing whitespace
borg/localrole/workspace.py:116:1: W293 blank line contains whitespace
borg/localrole/workspace.py:119:1: W293 blank line contains whitespace
borg/localrole/workspace.py:120:59: E202 whitespace before ')'
borg/localrole/workspace.py:124:80: E501 line too long (80 > 79 characters)
borg/localrole/workspace.py:125:80: E501 line too long (81 > 79 characters)
borg/localrole/workspace.py:127:1: W293 blank line contains whitespace
borg/localrole/workspace.py:128:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:128:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:129:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:140:1: E305 expected 2 blank lines after class or function definition, found 1
```
Follow [these instructions](https://github.com/plone/jenkins.plone.org/blob/master/docs/source/run-qa-on-package.rst) to reproduce it locally.


@optilude Jenkins CI reporting about code analysis
See the full report here: http://jenkins.plone.org/job/package-borg.localrole/3/violations
```
borg/__init__.py:0:1: C101 Coding magic comment not found
borg/localrole/config.py:0:1: C101 Coding magic comment not found
borg/localrole/config.py:3:42: W292 no newline at end of file
borg/localrole/tests.py:0:1: C101 Coding magic comment not found
borg/localrole/tests.py:1:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:2:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:3:1: I004 isort found an unexpected blank line in imports
borg/localrole/tests.py:4:1: F401 'zope.testing.doctestunit' imported but unused
borg/localrole/tests.py:4:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:5:1: F401 'zope.component.testing' imported but unused
borg/localrole/tests.py:5:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:6:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:7:1: I004 isort found an unexpected blank line in imports
borg/localrole/tests.py:9:1: I001 isort found an import in the wrong position
borg/localrole/tests.py:10:1: I004 isort found an unexpected blank line in imports
borg/localrole/tests.py:15:1: I003 isort expected 1 blank line in imports, found 0
borg/localrole/tests.py:18:1: E302 expected 2 blank lines, found 1
borg/localrole/tests.py:27:1: E302 expected 2 blank lines, found 1
borg/localrole/tests.py:33:44: W291 trailing whitespace
borg/localrole/tests.py:36:1: W293 blank line contains whitespace
borg/localrole/tests.py:39:1: E305 expected 2 blank lines after class or function definition, found 1
borg/localrole/interfaces.py:0:1: C101 Coding magic comment not found
borg/localrole/interfaces.py:2:1: I003 isort expected 1 blank line in imports, found 0
borg/localrole/interfaces.py:3:1: E302 expected 2 blank lines, found 1
borg/localrole/interfaces.py:5:1: W293 blank line contains whitespace
borg/localrole/interfaces.py:6:74: W291 trailing whitespace
borg/localrole/interfaces.py:7:72: W291 trailing whitespace
borg/localrole/interfaces.py:10:1: W293 blank line contains whitespace
borg/localrole/interfaces.py:20:1: E302 expected 2 blank lines, found 1
borg/localrole/interfaces.py:22:1: W293 blank line contains whitespace
borg/localrole/interfaces.py:26:1: W293 blank line contains whitespace
borg/localrole/interfaces.py:30:8: W292 no newline at end of file
borg/localrole/__init__.py:0:1: C101 Coding magic comment not found
borg/localrole/__init__.py:2:1: I001 isort found an import in the wrong position
borg/localrole/__init__.py:4:1: I001 isort found an import in the wrong position
borg/localrole/__init__.py:8:1: E302 expected 2 blank lines, found 1
borg/localrole/__init__.py:11:1: W293 blank line contains whitespace
borg/localrole/__init__.py:13:37: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:13:39: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:14:39: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:14:41: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:14:80: E501 line too long (92 > 79 characters)
borg/localrole/__init__.py:15:80: E501 line too long (89 > 79 characters)
borg/localrole/__init__.py:16:37: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:16:39: E251 unexpected spaces around keyword / parameter equals
borg/localrole/__init__.py:16:45: W292 no newline at end of file
borg/localrole/utils.py:0:1: C101 Coding magic comment not found
borg/localrole/utils.py:3:1: I001 isort found an import in the wrong position
borg/localrole/utils.py:4:1: I001 isort found an import in the wrong position
borg/localrole/utils.py:5:1: I004 isort found an unexpected blank line in imports
borg/localrole/utils.py:6:1: I001 isort found an import in the wrong position
borg/localrole/utils.py:8:1: E302 expected 2 blank lines, found 1
borg/localrole/utils.py:12:1: W293 blank line contains whitespace
borg/localrole/utils.py:22:9: T001 print statement found.
borg/localrole/utils.py:22:23: Q000 Remove bad quotes.
borg/localrole/utils.py:22:23: S001 found module formatter
borg/localrole/utils.py:23:1: W293 blank line contains whitespace
borg/localrole/utils.py:24:26: W292 no newline at end of file
borg/localrole/workspace.py:0:1: C101 Coding magic comment not found
borg/localrole/workspace.py:7:1: F401 'Acquisition.aq_chain' imported but unused
borg/localrole/workspace.py:7:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:8:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:11:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:12:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:13:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:14:1: I004 isort found an unexpected blank line in imports
borg/localrole/workspace.py:15:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:16:1: I001 isort found an import in the wrong position
borg/localrole/workspace.py:19:9: Q000 Remove bad quotes.
borg/localrole/workspace.py:20:18: Q000 Remove bad quotes.
borg/localrole/workspace.py:22:1: E302 expected 2 blank lines, found 1
borg/localrole/workspace.py:22:80: E501 line too long (82 > 79 characters)
borg/localrole/workspace.py:23:80: E501 line too long (81 > 79 characters)
borg/localrole/workspace.py:29:17: S001 found module formatter
borg/localrole/workspace.py:29:80: E501 line too long (90 > 79 characters)
borg/localrole/workspace.py:32:1: E302 expected 2 blank lines, found 1
borg/localrole/workspace.py:33:17: Q000 Remove bad quotes.
borg/localrole/workspace.py:34:13: E221 multiple spaces before operator
borg/localrole/workspace.py:44:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:44:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:45:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:57:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:57:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:58:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:60:1: W293 blank line contains whitespace
borg/localrole/workspace.py:65:1: W293 blank line contains whitespace
borg/localrole/workspace.py:72:1: W293 blank line contains whitespace
borg/localrole/workspace.py:75:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:75:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:76:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:78:1: W293 blank line contains whitespace
borg/localrole/workspace.py:82:1: W293 blank line contains whitespace
borg/localrole/workspace.py:84:1: W293 blank line contains whitespace
borg/localrole/workspace.py:86:1: W293 blank line contains whitespace
borg/localrole/workspace.py:87:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:87:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:88:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:93:1: W293 blank line contains whitespace
borg/localrole/workspace.py:99:1: W293 blank line contains whitespace
borg/localrole/workspace.py:100:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:100:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:101:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:102:73: W291 trailing whitespace
borg/localrole/workspace.py:105:1: W293 blank line contains whitespace
borg/localrole/workspace.py:111:75: W291 trailing whitespace
borg/localrole/workspace.py:112:77: W291 trailing whitespace
borg/localrole/workspace.py:116:1: W293 blank line contains whitespace
borg/localrole/workspace.py:119:1: W293 blank line contains whitespace
borg/localrole/workspace.py:120:59: E202 whitespace before ')'
borg/localrole/workspace.py:124:80: E501 line too long (80 > 79 characters)
borg/localrole/workspace.py:125:80: E501 line too long (81 > 79 characters)
borg/localrole/workspace.py:127:1: W293 blank line contains whitespace
borg/localrole/workspace.py:128:14: D001 found declarePrivate( replace it with AccessControl.ClassSecurityInfo.private
borg/localrole/workspace.py:128:29: Q000 Remove bad quotes.
borg/localrole/workspace.py:129:5: E301 expected 1 blank line, found 0
borg/localrole/workspace.py:140:1: E305 expected 2 blank lines after class or function definition, found 1
```
Follow [these instructions](https://github.com/plone/jenkins.plone.org/blob/master/docs/source/run-qa-on-package.rst) to reproduce it locally.