nebbiolo1 Summary
[top]
Package: RgnTX |
Version: 0.99.7 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RgnTX |
BuildTime: 5 minutes 12.49 seconds |
CheckCommand: BiocCheckGitClone('RgnTX') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings RgnTX_0.99.7.tar.gz && BiocCheck('RgnTX_0.99.7.tar.gz', `new-package`=TRUE) |
CheckTime: 7 minutes 4.66 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 3675.59 KiB |
BuildID:: RgnTX_20220519180840 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: RgnTX. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* preparing ‘RgnTX’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘RgnTX_0.99.7.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('RgnTX')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: RgnTX
─ PackageVersion: 0.99.7
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2635/fa97ea6abd20fcee254871f990e56c3661a9467b/RgnTX
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2635/fa97ea6abd20fcee254871f990e56c3661a9467b/RgnTX.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* this is package ‘RgnTX’ version ‘0.99.7’
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RgnTX’ can be installed ... [25s/25s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... OK
* checking R 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [27s/27s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [190s/190s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotShiftedZScoreTx 22.512 0.052 22.565
shiftedZScoreTx 22.377 0.064 22.442
plotPermResults 14.572 0.044 14.616
permTestTxIA 12.840 0.104 12.944
permTestTxIA_customPick 12.797 0.056 12.853
permTestTx 11.347 0.080 11.427
permTestTx_customPick 9.696 0.032 9.728
permTestTx_customAll 8.760 0.032 8.792
overlapCountsTxIA 5.046 0.019 5.067
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [41s/41s]
[41s/41s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
===============================
BiocCheck('RgnTX_0.99.7.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: RgnTX
─ PackageVersion: 0.99.7
─ sourceDir: /tmp/RtmpWWrmNT/file11ee164b029ef8/RgnTX
─ installDir: /tmp/RtmpWWrmNT/file11ee16e7db28a
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2635/fa97ea6abd20fcee254871f990e56c3661a9467b/RgnTX.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of RgnTX...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 6
functions > 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 521 lines (11%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 103 lines
(2%) are not.
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES
See the RgnTX.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]
merida1 Summary
[top]
Package: RgnTX |
Version: 0.99.7 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RgnTX |
BuildTime: 8 minutes 13.76 seconds |
CheckCommand: BiocCheckGitClone('RgnTX') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RgnTX_0.99.7.tar.gz && BiocCheck('RgnTX_0.99.7.tar.gz', `new-package`=TRUE) |
CheckTime: 10 minutes 12.63 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh RgnTX_0.99.7.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 35.71 seconds |
PackageFileSize: 3669.29 KiB |
BuildID:: RgnTX_20220519180840 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: RgnTX. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* preparing ‘RgnTX’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘RgnTX_0.99.7.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('RgnTX')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: RgnTX
─ PackageVersion: 0.99.7
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2635/fa97ea6abd20fcee254871f990e56c3661a9467b/RgnTX
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2635/fa97ea6abd20fcee254871f990e56c3661a9467b/RgnTX.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* this is package ‘RgnTX’ version ‘0.99.7’
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RgnTX’ can be installed ... [35s/35s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... OK
* checking R 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [37s/37s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [284s/284s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotShiftedZScoreTx 34.903 0.422 35.321
shiftedZScoreTx 34.581 0.350 34.930
plotPermResults 22.573 0.081 22.654
permTestTxIA_customPick 20.873 0.139 21.010
permTestTxIA 20.675 0.152 20.825
permTestTx 17.479 0.099 17.578
permTestTx_customPick 15.132 0.079 15.211
permTestTx_customAll 13.637 0.090 13.727
overlapCountsTxIA 7.913 0.100 8.012
distanceTx 6.656 0.097 6.754
overlapWidthTx 6.383 0.081 6.464
getStopCodon 6.334 0.071 6.403
randomizeFeaturesTx 6.096 0.060 6.155
getFormatCorrect 5.975 0.044 6.018
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [57s/57s]
[58s/58s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
===============================
BiocCheck('RgnTX_0.99.7.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: RgnTX
─ PackageVersion: 0.99.7
─ sourceDir: /tmp/Rtmpt9Pzov/file42a22a9cb2ce/RgnTX
─ installDir: /tmp/Rtmpt9Pzov/file42a27bd5e7e1
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2635/fa97ea6abd20fcee254871f990e56c3661a9467b/RgnTX.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of RgnTX...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 6
functions > 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 521 lines (11%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 103 lines
(2%) are not.
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES
See the RgnTX.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir RgnTX_0.99.7.tar.gz'
>>>>>>>
* installing *source* package ‘RgnTX’ ...
** 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 (RgnTX)