Thomas Girke
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024) |
| git_url: https://git.bioconductor.org/packages/systemPipeR |
| git_branch: devel |
| git_last_commit: 55f5649 |
| git_last_commit_date: 2024-04-30 10:38:46 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:21 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2060/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| systemPipeR 2.11.0 (landing page) Thomas Girke
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the systemPipeR package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: systemPipeR |
| Version: 2.11.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings systemPipeR_2.11.0.tar.gz |
| StartedAt: 2024-05-20 04:44:10 -0400 (Mon, 20 May 2024) |
| EndedAt: 2024-05-20 04:50:41 -0400 (Mon, 20 May 2024) |
| EllapsedTime: 390.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: systemPipeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings systemPipeR_2.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/systemPipeR.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘systemPipeR’ version ‘2.11.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
inst/extdata/.batchtools.conf.R
inst/extdata/.batchtools.conf.R.sge
inst/extdata/.batchtools.conf.R.torque
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘systemPipeR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
R 1.6Mb
extdata 2.7Mb
htmlwidgets 2.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
OVERVIEW
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.cmd2cwl2: no visible global function definition for ‘ave’
.getPreprotext: no visible binding for global variable ‘.’
Undefined global functions or variables:
. ave
Consider adding
importFrom("stats", "ave")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
genFeatures 33.485 0.521 34.193
run_DESeq2 9.578 0.298 9.925
loadWorkflow 5.940 0.117 6.078
renderLogs 4.462 0.797 5.542
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/systemPipeR.Rcheck/00check.log’
for details.
systemPipeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL systemPipeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘systemPipeR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (systemPipeR)
systemPipeR.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(systemPipeR)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>
> test_check("systemPipeR")
[1] "Generated /tmp/RtmpEg6tuO/rnaseq directory. Next run in rnaseq directory, the R code from *.Rmd template interactively. Alternatively, workflows can be exectued with a single command as instructed in the vignette."
[1] "Generated /tmp/RtmpEg6tuO/rnaseq2 directory. Next run in rnaseq directory, the R code from *.Rmd template interactively. Alternatively, workflows can be exectued with a single command as instructed in the vignette."
Creating directory '/private/tmp/RtmpEg6tuO/rnaseq2/.SPRproject'
Creating file '/private/tmp/RtmpEg6tuO/rnaseq2/.SPRproject/SYSargsList.yml'
Running Step: example
Running Session: Management
|
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|======================= | 33%
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|=============================================== | 67%
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|======================================================================| 100%
---- Summary ----
Targets Total_Files Existing_Files Missing_Files example
M1 M1 1 1 0 Success
M2 M2 1 1 0 Success
M3 M3 1 1 0 Success
Step Status: Success
Done with workflow running, now consider rendering logs & reports
To render logs, run: sal <- renderLogs(sal)
From command-line: Rscript -e "sal = systemPipeR::SPRproject(resume = TRUE); sal = systemPipeR::renderLogs(sal)"
To render reports, run: sal <- renderReport(sal)
From command-line: Rscript -e "sal= s ystemPipeR::SPRproject(resume = TRUE); sal = systemPipeR::renderReport(sal)"
This message is displayed once per R session
Running Step: newStep
Running Session: Management
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
---- Summary ----
Targets Total_Files Existing_Files Missing_Files example
M1 M1 1 1 0 Success
M2 M2 1 1 0 Success
M3 M3 1 1 0 Success
Step Status: Success
Running Step: R_code
Running Session: Management
|
| | 0%
|
|======================================================================| 100%
Step Status: Warning
[1] "Generated /tmp/RtmpEg6tuO/newtest directory. Next run in new directory, the R code from *.Rmd template interactively. Alternatively, workflows can be exectued with a single command as instructed in the vignette."
Creating directory '/private/tmp/RtmpEg6tuO/newtest/.SPRproject'
Creating file '/private/tmp/RtmpEg6tuO/newtest/.SPRproject/SYSargsList.yml'
Reading Rmd file
Now importing step 'load_library'
Now importing step 'export_iris'
Now importing step 'gzip'
Now importing step 'gunzip'
Now importing step 'stats'
Now back up current Rmd file as template for `renderReport`
Template for renderReport is stored at
/private/tmp/RtmpEg6tuO/newtest/.SPRproject/workflow_template.Rmd
Edit this file manually is not recommended
Now check if required tools are installed
Check if they are in path:
Checking path for gzip
PASS
Checking path for gunzip
PASS
step_name tool in_path
1 gzip gzip TRUE
2 gunzip gunzip TRUE
All required tools in PATH, skip module check. If you want to check modules use `listCmdModules`Import done
Instance of 'LineWise'
Code Chunk length: 1
mapply(function(x, y) write.csv(x, y), split(iris, factor(iris$Species)), file.path("results", paste0(names(split(iris, factor(iris$Species))), ".csv")))
load_library
5 + 5
load_library
5 + 5
66 + 55
Running Step: load_library
Running Session: Management
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|======================================================================| 100%
Step Status: Success
Running Step: export_iris
Running Session: Management
|
| | 0%
|
|======================================================================| 100%
Step Status: Success
Skipping Step: gzip
Skipping Step: gunzip
Skipping Step: stats
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 47 ]
══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On Bioconductor (10): 'test-01-SYSargs.R:2:1', 'test-02-SYSargs2.R:9:5',
'test-02-SYSargs2.R:55:5', 'test-03-SYSargsList.R:63:5',
'test-05-catDB.R:3:1', 'test-06-VENNset.R:3:1', 'test-07-features.R:3:1',
'test-08-cmd2cwl.R:2:1', 'test-10-chipSeq.R:4:1', 'test-utilities.R:2:1'
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 47 ]
>
> proc.time()
user system elapsed
14.718 1.956 16.987
systemPipeR.Rcheck/systemPipeR-Ex.timings
| name | user | system | elapsed | |
| EnvModules-class | 0.001 | 0.001 | 0.001 | |
| GOHyperGAll | 0.001 | 0.001 | 0.001 | |
| INTERSECTset-class | 0.008 | 0.008 | 0.017 | |
| LineWise-class | 0.151 | 0.021 | 0.175 | |
| ParamFiles | 0.087 | 0.004 | 0.091 | |
| ParamFiles2 | 0.129 | 0.004 | 0.136 | |
| SPRproject | 0.004 | 0.002 | 0.005 | |
| SYSargs-class | 0.022 | 0.008 | 0.029 | |
| SYSargs2-class | 0.060 | 0.007 | 0.070 | |
| SYSargsList-class | 0.598 | 0.053 | 0.670 | |
| SYSargsList | 0.092 | 0.008 | 0.101 | |
| VENNset-class | 0.005 | 0.004 | 0.009 | |
| alignStats | 1.944 | 0.041 | 2.036 | |
| catDB-class | 0.000 | 0.000 | 0.001 | |
| catmap | 0.000 | 0.001 | 0.001 | |
| check.output | 1.158 | 0.029 | 1.193 | |
| clusterRun | 1.088 | 0.010 | 1.102 | |
| config.param | 0.000 | 0.000 | 0.001 | |
| configWF | 0.000 | 0.000 | 0.001 | |
| countRangeset | 0.038 | 0.002 | 0.042 | |
| createParamFiles | 0.131 | 0.002 | 0.134 | |
| cwlFilesUpdate | 0 | 0 | 0 | |
| evalCode | 0.028 | 0.005 | 0.035 | |
| featureCoverage | 1.083 | 0.005 | 1.092 | |
| featuretypeCounts | 1.084 | 0.006 | 1.095 | |
| filterDEGs | 1.789 | 0.039 | 1.840 | |
| filterVars | 0.009 | 0.003 | 0.012 | |
| genFeatures | 33.485 | 0.521 | 34.193 | |
| importWF | 0.041 | 0.012 | 0.061 | |
| listCmdTools | 0 | 0 | 0 | |
| loadWorkflow | 5.940 | 0.117 | 6.078 | |
| mergeBamByFactor | 0.009 | 0.003 | 0.012 | |
| moduleload | 0.000 | 0.001 | 0.000 | |
| olBarplot | 0.670 | 0.041 | 0.713 | |
| olRanges | 0.117 | 0.003 | 0.120 | |
| output_update | 1.076 | 0.007 | 1.086 | |
| overLapper | 0.337 | 0.026 | 0.365 | |
| plotfeatureCoverage | 1.279 | 0.007 | 1.296 | |
| plotfeaturetypeCounts | 0.943 | 0.009 | 0.997 | |
| predORF | 0.141 | 0.003 | 0.150 | |
| preprocessReads | 0.371 | 0.006 | 0.389 | |
| readComp | 1.089 | 0.007 | 1.103 | |
| renderLogs | 4.462 | 0.797 | 5.542 | |
| renderReport | 1.588 | 0.433 | 2.167 | |
| returnRPKM | 0 | 0 | 0 | |
| runCommandline | 1.353 | 0.247 | 1.606 | |
| runDiff | 0.032 | 0.004 | 0.035 | |
| runWF | 0.093 | 0.011 | 0.107 | |
| run_DESeq2 | 9.578 | 0.298 | 9.925 | |
| run_edgeR | 1.302 | 0.026 | 1.343 | |
| sal2bash | 0.463 | 0.090 | 0.566 | |
| sal2rmd | 0.501 | 0.172 | 0.684 | |
| scaleRanges | 0.191 | 0.048 | 0.241 | |
| seeFastq | 0 | 0 | 0 | |
| showDF | 0.056 | 0.039 | 0.096 | |
| subsetWF | 1.346 | 0.279 | 1.639 | |
| symLink2bam | 1.099 | 0.103 | 1.210 | |
| sysargs | 0.011 | 0.004 | 0.016 | |
| systemArgs | 0.010 | 0.004 | 0.013 | |
| targets.as.df | 0.004 | 0.002 | 0.006 | |
| trimbatch | 0.247 | 0.009 | 0.256 | |
| tryCMD | 0 | 0 | 0 | |
| tryPath | 0.002 | 0.001 | 0.003 | |
| variantReport | 0.008 | 0.003 | 0.012 | |
| vennPlot | 0.568 | 0.038 | 0.628 | |
| writeTargets | 0.092 | 0.010 | 0.102 | |
| writeTargetsRef | 0.002 | 0.001 | 0.002 | |
| writeTargetsout | 1.084 | 0.007 | 1.095 | |
| write_SYSargsList | 0.112 | 0.010 | 0.123 | |