lconway Summary
[top]
| Package: iNETgrate |
| Version: 0.99.74 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data iNETgrate |
| BuildTime: 3 minutes 40.98 seconds |
| CheckCommand: BiocCheckGitClone('iNETgrate') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2979/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2979/9a5a9aa0f2f643408de62b070a864b9ea2e5dbf7/iNETgrate.install-out.txt iNETgrate_0.99.74.tar.gz && BiocCheck('iNETgrate_0.99.74.tar.gz', `new-package`=TRUE) |
| CheckTime: 14 minutes 26.06 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh iNETgrate_0.99.74.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 58.78 seconds |
| PackageFileSize: 4597.82 KiB |
| BuildID:: iNETgrate_20230524234358 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: iNETgrate. 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. WARNING: check time exceeded 10 min. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘iNETgrate/DESCRIPTION’ ... OK
* preparing ‘iNETgrate’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* excluding invalid files
Subdirectory 'R' contains invalid file names:
‘downloaData.Rd’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘iNETgrate/data/toyCleanedAml.rda’
‘iNETgrate/data/toyComputEloci.rda’
‘iNETgrate/data/toyEigengenes.rda’ ‘iNETgrate/data/toyRawAml.rda’
* building ‘iNETgrate_0.99.74.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('iNETgrate')
===============================
─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: iNETgrate
─ PackageVersion: 0.99.74
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2979/9a5a9aa0f2f643408de62b070a864b9ea2e5dbf7/iNETgrate
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc 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/2979/9a5a9aa0f2f643408de62b070a864b9ea2e5dbf7/iNETgrate.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iNETgrate/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iNETgrate’ version ‘0.99.74’
* 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 ‘iNETgrate’ can be installed ... 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 ... [18s/19s] OK
* checking whether the package can be loaded with stated dependencies ... [18s/18s] OK
* checking whether the package can be unloaded cleanly ... [17s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [17s/17s] OK
* checking loading without being on the library search path ... [17s/17s] 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 ... [60s/61s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'prepareSurvival.Rd':
‘downloaData’
Missing link or links in documentation object 'sampleData.Rd':
‘downloaData’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
toyCleanedAml.rda 1.9Mb 1.7Mb xz
toyComputEloci.rda 115Kb 103Kb xz
toyRawAml.rda 2.1Mb 1.8Mb xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [464s/464s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
iNETgrate 107.339 1.570 109.019
computeEigengenes 59.533 0.079 59.630
toyEigengenes 56.184 0.095 56.300
analyzeSurvival 48.062 0.268 47.917
toyComputEloci 40.037 1.267 41.392
makeNetwork 36.431 0.043 36.485
computeEigenloci 12.501 0.541 13.091
cleanAllData 11.094 0.418 11.518
accelFailAnalysis 5.513 0.135 5.556
* 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 ... [8s/9s] OK
* DONE
Status: 2 WARNINGs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2979/9a5a9aa0f2f643408de62b070a864b9ea2e5dbf7/iNETgrate.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('iNETgrate_0.99.74.tar.gz')
===============================
─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: iNETgrate
─ PackageVersion: 0.99.74
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp7kCUV0/file1685f8a1e9e5/iNETgrate
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp7kCUV0/file1685f25fbc27e
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2979/9a5a9aa0f2f643408de62b070a864b9ea2e5dbf7/iNETgrate.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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 3.5.0 to 4.3.0.
* 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...
* 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 iNETgrate...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 23 functions greater than 50 lines.
* Checking man page documentation...
Registered S3 method overwritten by 'gplots':
method from
reorder.factor gdata
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 6% of man pages use at least one of these tags.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 694 lines (11%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1022 lines
(16%) are not.
See https://contributions.bioconductor.org/r-code.html
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 | 8 NOTES
See the iNETgrate.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir iNETgrate_0.99.74.tar.gz'
>>>>>>>
* installing *source* package ‘iNETgrate’ ...
** using staged installation
** R
** data
** 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 (iNETgrate)
nebbiolo2 Summary
[top]
| Package: iNETgrate |
| Version: 0.99.74 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data iNETgrate |
| BuildTime: 3 minutes 56.12 seconds |
| CheckCommand: BiocCheckGitClone('iNETgrate') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2979/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2979/9a5a9aa0f2f643408de62b070a864b9ea2e5dbf7/iNETgrate.install-out.txt iNETgrate_0.99.74.tar.gz && BiocCheck('iNETgrate_0.99.74.tar.gz', `new-package`=TRUE) |
| CheckTime: 15 minutes 0.00 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4597.52 KiB |
| BuildID:: iNETgrate_20230524234358 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: iNETgrate. 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: -9. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘iNETgrate/DESCRIPTION’ ... OK
* preparing ‘iNETgrate’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* excluding invalid files
Subdirectory 'R' contains invalid file names:
‘downloaData.Rd’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘iNETgrate/data/toyCleanedAml.rda’
‘iNETgrate/data/toyComputEloci.rda’
‘iNETgrate/data/toyEigengenes.rda’ ‘iNETgrate/data/toyRawAml.rda’
* building ‘iNETgrate_0.99.74.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('iNETgrate')
===============================
─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: iNETgrate
─ PackageVersion: 0.99.74
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2979/9a5a9aa0f2f643408de62b070a864b9ea2e5dbf7/iNETgrate
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc 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/2979/9a5a9aa0f2f643408de62b070a864b9ea2e5dbf7/iNETgrate.Rcheck’
* using R version 4.3.0 RC (2023-04-18 r84287)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iNETgrate/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iNETgrate’ version ‘0.99.74’
* 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 ‘iNETgrate’ can be installed ... 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 ... [18s/18s] OK
* checking whether the package can be loaded with stated dependencies ... [19s/19s] OK
* checking whether the package can be unloaded cleanly ... [18s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [19s/19s] OK
* checking whether the namespace can be unloaded cleanly ... [20s/20s] OK
* checking loading without being on the library search path ... [19s/19s] 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 ... [66s/66s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'prepareSurvival.Rd':
‘downloaData’
Missing link or links in documentation object 'sampleData.Rd':
‘downloaData’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
toyCleanedAml.rda 1.9Mb 1.7Mb xz
toyComputEloci.rda 115Kb 103Kb xz
toyRawAml.rda 2.1Mb 1.8Mb xz
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('iNETgrate_0.99.74.tar.gz')
===============================
[527s/526s]─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: iNETgrate
─ PackageVersion: 0.99.74
─ sourceDir: /tmp/RtmpzlT1Zm/file2550d1311d19f2/iNETgrate
─ installDir: /tmp/RtmpzlT1Zm/file2550d13b3da2fe
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2979/9a5a9aa0f2f643408de62b070a864b9ea2e5dbf7/iNETgrate.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
iNETgrate 119.753 0.980 120.735
toyEigengenes 65.215 0.352 65.566
computeEigengenes 64.885 0.513 65.399
analyzeSurvival 53.169 0.631 53.297
makeNetwork 44.728 0.241 44.967
toyComputEloci 44.325 0.560 44.889
computeEigenloci 14.476 0.448 14.924
cleanAllData 14.198 0.616 14.796
accelFailAnalysis 6.253 0.193 6.336
* 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 ...* 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 3.5.0 to 4.3.0.
* Checking package size...
[4s/4s] OK
* DONE
Status: 2 WARNINGs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2979/9a5a9aa0f2f643408de62b070a864b9ea2e5dbf7/iNETgrate.Rcheck/00check.log’
for details.
* 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 iNETgrate...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 23 functions greater than 50 lines.
* Checking man page documentation...
Registered S3 method overwritten by 'gplots':
method from
reorder.factor gdata
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 6% of man pages use at least one of these tags.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 694 lines (11%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1022 lines
(16%) are not.
See https://contributions.bioconductor.org/r-code.html
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 | 8 NOTES
See the iNETgrate.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]