nebbiolo2 Summary
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| Package: curatedPCaData |
| Version: 0.99.3 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data curatedPCaData |
| BuildTime: 6 minutes 43.45 seconds |
| CheckCommand: BiocCheckGitClone('curatedPCaData') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3047/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3047/dc4bdc2415d75312999a5d10a986720068f77100/curatedPCaData.install-out.txt curatedPCaData_0.99.3.tar.gz && BiocCheck('curatedPCaData_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 16 minutes 4.26 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2894.55 KiB |
| BuildID:: curatedPCaData_20230809225243 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: curatedPCaData. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘curatedPCaData/DESCRIPTION’ ... OK
* preparing ‘curatedPCaData’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘curatedPCaData_0.99.3.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('curatedPCaData')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: curatedPCaData
─ PackageVersion: 0.99.3
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3047/dc4bdc2415d75312999a5d10a986720068f77100/curatedPCaData
─ 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/3047/dc4bdc2415d75312999a5d10a986720068f77100/curatedPCaData.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘curatedPCaData/DESCRIPTION’ ... OK
* this is package ‘curatedPCaData’ version ‘0.99.3’
* 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 ‘curatedPCaData’ 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [35s/35s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [421s/472s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getPCaSummaryStudies 165.304 5.944 191.577
getPCaSummaryTable 22.849 0.688 26.130
getPCaSummarySurv 22.829 0.684 26.021
getPCaSummarySamples 19.115 0.369 22.460
curatedPCaDatasets_abida 13.509 0.852 15.787
getPCa 9.341 0.200 10.886
curatedPCaDatasets_taylor 9.310 0.208 10.974
curatedPCaDatasets_barbieri 9.033 0.312 10.699
curatedPCaDatasets_tcga 8.994 0.220 10.477
curatedPCaDatasets_chandran 7.974 0.244 9.263
curatedPCaDatasets_ren 8.053 0.160 9.396
curatedPCaDatasets_weiner 7.886 0.263 9.288
curatedPCaDatasets_friedrich 7.589 0.252 8.909
curatedPCaDatasets_icgcca 7.392 0.147 8.622
curatedPCaDatasets_kim 7.286 0.125 8.537
curatedPCaDatasets_igc 7.158 0.224 8.458
curatedPCaDatasets_kunderfranco 7.106 0.196 8.402
curatedPCaDatasets_sun 7.160 0.088 8.432
curatedPCaDatasets_wang 7.043 0.120 8.249
curatedPCaDatasets_wallace 6.969 0.160 8.319
curatedPCaDatasets_true 6.293 0.101 7.443
curatedPCaDatasets_barwick 5.892 0.168 7.134
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘native_tests.R’ [244s/269s]
[244s/269s] 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 ... [4s/4s] OK
* DONE
Status: OK
===============================
BiocCheck('curatedPCaData_0.99.3.tar.gz')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: curatedPCaData
─ PackageVersion: 0.99.3
─ sourceDir: /tmp/Rtmpc44lFM/file16a1ab7e5e74d0/curatedPCaData
─ installDir: /tmp/Rtmpc44lFM/file16a1ab68b7717f
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3047/dc4bdc2415d75312999a5d10a986720068f77100/curatedPCaData.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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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 curatedPCaData...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 3 functions greater than 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; 12 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 11 lines
(0%) 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 | 3 NOTES
See the curatedPCaData.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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lconway Summary
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| Package: curatedPCaData |
| Version: 0.99.3 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data curatedPCaData |
| BuildTime: 6 minutes 37.68 seconds |
| CheckCommand: BiocCheckGitClone('curatedPCaData') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3047/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3047/dc4bdc2415d75312999a5d10a986720068f77100/curatedPCaData.install-out.txt curatedPCaData_0.99.3.tar.gz && BiocCheck('curatedPCaData_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 17 minutes 54.50 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh curatedPCaData_0.99.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 48.52 seconds |
| PackageFileSize: 2894.46 KiB |
| BuildID:: curatedPCaData_20230809225243 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: curatedPCaData. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘curatedPCaData/DESCRIPTION’ ... OK
* preparing ‘curatedPCaData’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘curatedPCaData_0.99.3.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('curatedPCaData')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: curatedPCaData
─ PackageVersion: 0.99.3
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3047/dc4bdc2415d75312999a5d10a986720068f77100/curatedPCaData
─ 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/3047/dc4bdc2415d75312999a5d10a986720068f77100/curatedPCaData.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* 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 ‘curatedPCaData/DESCRIPTION’ ... OK
* this is package ‘curatedPCaData’ version ‘0.99.3’
* 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 ‘curatedPCaData’ 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [11s/11s] 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/38s] OK
* checking Rd files ... [1s/1s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [505s/561s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getPCaSummaryStudies 176.384 12.321 210.914
getPCaSummaryTable 24.815 1.876 29.584
getPCaSummarySamples 23.942 1.678 28.491
getPCaSummarySurv 22.264 1.658 26.784
curatedPCaDatasets_abida 15.438 1.484 18.510
getPCa 12.895 0.914 15.307
curatedPCaDatasets_taylor 12.166 0.876 14.522
curatedPCaDatasets_tcga 12.066 0.839 14.418
curatedPCaDatasets_true 10.828 0.844 12.979
curatedPCaDatasets_barbieri 10.658 0.779 12.925
curatedPCaDatasets_chandran 10.610 0.775 12.569
curatedPCaDatasets_ren 10.280 0.711 12.210
curatedPCaDatasets_weiner 9.845 0.715 11.725
curatedPCaDatasets_igc 9.593 0.726 11.531
curatedPCaDatasets_wallace 9.299 0.680 11.163
curatedPCaDatasets_icgcca 9.293 0.685 11.111
curatedPCaDatasets_kunderfranco 9.226 0.692 11.189
curatedPCaDatasets_sun 9.029 0.690 10.895
curatedPCaDatasets_kim 9.032 0.658 10.798
curatedPCaDatasets_friedrich 8.896 0.665 10.762
curatedPCaDatasets_wang 8.842 0.660 10.725
curatedPCaDatasets_barwick 7.865 0.620 9.623
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘native_tests.R’ [250s/276s]
[250s/276s] 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 ... [6s/6s] OK
* DONE
Status: OK
===============================
BiocCheck('curatedPCaData_0.99.3.tar.gz')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: curatedPCaData
─ PackageVersion: 0.99.3
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpPwgkmj/filec8c218df58ee/curatedPCaData
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpPwgkmj/filec8c23ea23008
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3047/dc4bdc2415d75312999a5d10a986720068f77100/curatedPCaData.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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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 curatedPCaData...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 3 functions greater than 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; 12 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 11 lines
(0%) 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 | 3 NOTES
See the curatedPCaData.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir curatedPCaData_0.99.3.tar.gz'
>>>>>>>
* installing *source* package ‘curatedPCaData’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (curatedPCaData)