nebbiolo1 Summary
[top]
| Package: octad |
| Version: 0.99.79 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data octad |
| BuildTime: 2 minutes 18.10 seconds |
| CheckCommand: BiocCheckGitClone('octad') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings octad_0.99.79.tar.gz && BiocCheck('octad_0.99.79.tar.gz', `new-package`=TRUE) |
| CheckTime: 8 minutes 42.08 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 244.17 KiB |
| BuildID:: octad_20220426044522 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: octad. 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 ‘octad/DESCRIPTION’ ... OK
* preparing ‘octad’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘octad_0.99.79.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('octad')
===============================
─ BiocCheckVersion: 1.31.39
─ BiocVersion: 3.15
─ Package: octad
─ PackageVersion: 0.99.79
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2391/7c51a3ed84189a43dadba42ba5b23b37ca6eb90b/octad
─ 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...
* Checking that provided CITATION file is correctly formatted...
─ 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/2391/7c51a3ed84189a43dadba42ba5b23b37ca6eb90b/octad.Rcheck’
* using R version 4.2.0 RC (2022-04-19 r82224)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘octad/DESCRIPTION’ ... OK
* this is package ‘octad’ version ‘0.99.79’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'magrittr', 'dplyr', 'ggplot2', 'edgeR', 'RUVSeq', 'DESeq2', 'limma',
'rhdf5', 'foreach', 'Rfast', 'octad.db', 'httr', 'ExperimentHub',
'AnnotationHub', 'Biobase', 'S4Vectors'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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:
.BBSoptions
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 ‘octad’ can be installed ... [36s/38s] 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 ... [39s/41s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'computeCellLine.Rd':
\usage lines wider than 90 characters:
computeCellLine(case_id =case_id,expSet=NULL,LINCS_overlaps = TRUE, source='octad.small',file=NULL,output = FALSE,outputFolder='')
Rd file 'octadDrugEnrichment.Rd':
\usage lines wider than 90 characters:
octadDrugEnrichment(sRGES=NULL,target_type='chembl_targets',enrichFolder='enrichFolder',outputFolder=NULL)
These lines will be truncated in the PDF manual.
* 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 ... [223s/224s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runsRGES 93.793 3.295 97.930
octadDrugEnrichment 28.153 3.900 30.352
computeCellLine 28.952 1.479 32.398
topLineEval 23.881 1.143 22.028
diffExp 14.754 0.496 16.230
* 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2391/7c51a3ed84189a43dadba42ba5b23b37ca6eb90b/octad.Rcheck/00check.log’
for details.
===============================
BiocCheck('octad_0.99.79.tar.gz')
===============================
─ BiocCheckVersion: 1.31.39
─ BiocVersion: 3.15
─ Package: octad
─ PackageVersion: 0.99.79
─ sourceDir: /tmp/Rtmpw1XfNO/file2c02408988f26/octad
─ installDir: /tmp/Rtmpw1XfNO/file2c02404978fc5d
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2391/7c51a3ed84189a43dadba42ba5b23b37ca6eb90b/octad.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...
* NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
Transcription, Sequencing, Epigenetics, Transcriptomics,
Coverage, Normalization, Pathways, Preprocessing, Bayesian,
Clustering, Regression, DNAMethylation, RNASeq, ChIPSeq,
CellBiology, BiomedicalInformatics, FunctionalGenomics,
SystemsBiology, ImmunoOncology, AlternativeSplicing,
DifferentialExpression, DifferentialMethylation,
DifferentialSplicing, BatchEffect, MultipleComparison,
QualityControl, TimeCourse, ThirdPartyClient, DataImport, GUI
Search 'biocViews' at https://contributions.bioconductor.org
* 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 octad...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 1 times)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 17
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 7
functions > 50 lines.
* Checking man page documentation...
snapshotDate(): 2022-04-19
snapshotDate(): 2022-04-19
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 263 lines (17%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 499 lines
(33%) 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 | 9 NOTES
See the octad.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: octad |
| Version: 0.99.79 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data octad |
| BuildTime: 7 minutes 6.58 seconds |
| CheckCommand: BiocCheckGitClone('octad') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch octad_0.99.79.tar.gz && BiocCheck('octad_0.99.79.tar.gz', `new-package`=TRUE) |
| CheckTime: 14 minutes 59.95 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh octad_0.99.79.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 2 minutes 46.98 seconds |
| PackageFileSize: 244.07 KiB |
| BuildID:: octad_20220426044522 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: octad. 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: -9. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘octad/DESCRIPTION’ ... OK
* preparing ‘octad’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘octad_0.99.79.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('octad')
===============================
─ BiocCheckVersion: 1.31.39
─ BiocVersion: 3.15
─ Package: octad
─ PackageVersion: 0.99.79
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2391/7c51a3ed84189a43dadba42ba5b23b37ca6eb90b/octad
─ 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...
* Checking that provided CITATION file is correctly formatted...
─ 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/2391/7c51a3ed84189a43dadba42ba5b23b37ca6eb90b/octad.Rcheck’
* using R version 4.2.0 RC (2022-04-19 r82224)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘octad/DESCRIPTION’ ... OK
* this is package ‘octad’ version ‘0.99.79’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'magrittr', 'dplyr', 'ggplot2', 'edgeR', 'RUVSeq', 'DESeq2', 'limma',
'rhdf5', 'foreach', 'Rfast', 'octad.db', 'httr', 'ExperimentHub',
'AnnotationHub', 'Biobase', 'S4Vectors'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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:
.BBSoptions
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 ‘octad’ can be installed ... [98s/99s] 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 ... [107s/114s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'computeCellLine.Rd':
\usage lines wider than 90 characters:
computeCellLine(case_id =case_id,expSet=NULL,LINCS_overlaps = TRUE, source='octad.small',file=NULL,output = FALSE,outputFolder='')
Rd file 'octadDrugEnrichment.Rd':
\usage lines wider than 90 characters:
octadDrugEnrichment(sRGES=NULL,target_type='chembl_targets',enrichFolder='enrichFolder',outputFolder=NULL)
These lines will be truncated in the PDF manual.
* 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 ... ERROR
TIMEOUT: R CMD check exceeded 14 mins
===============================
BiocCheck('octad_0.99.79.tar.gz')
===============================
─ BiocCheckVersion: 1.31.39
─ BiocVersion: 3.15
─ Package: octad
─ PackageVersion: 0.99.79
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp6Bh4tB/filea5071fa1310f/octad
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp6Bh4tB/filea507428fab4f
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2391/7c51a3ed84189a43dadba42ba5b23b37ca6eb90b/octad.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...
* NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
Transcription, Sequencing, Epigenetics, Transcriptomics,
Coverage, Normalization, Pathways, Preprocessing, Bayesian,
Clustering, Regression, DNAMethylation, RNASeq, ChIPSeq,
CellBiology, BiomedicalInformatics, FunctionalGenomics,
SystemsBiology, ImmunoOncology, AlternativeSplicing,
DifferentialExpression, DifferentialMethylation,
DifferentialSplicing, BatchEffect, MultipleComparison,
QualityControl, TimeCourse, ThirdPartyClient, DataImport, GUI
Search 'biocViews' at https://contributions.bioconductor.org
* 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 octad...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 1 times)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 17
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 7
functions > 50 lines.
* Checking man page documentation...
snapshotDate(): 2022-04-19
snapshotDate(): 2022-04-19
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 263 lines (17%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 499 lines
(33%) 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 | 9 NOTES
See the octad.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 octad_0.99.79.tar.gz'
>>>>>>>
* installing *source* package ‘octad’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
snapshotDate(): 2022-04-19
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2022-04-19
snapshotDate(): 2022-04-19
** testing if installed package can be loaded from final location
snapshotDate(): 2022-04-19
snapshotDate(): 2022-04-19
** testing if installed package keeps a record of temporary installation path
* DONE (octad)