nebbiolo2 Summary
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| Package: curatedPCaData |
| Version: 0.99.0 |
| 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: 7 minutes 42.15 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/curatedPCaData_20230530130915/curatedPCaData.install-out.txt curatedPCaData_0.99.0.tar.gz && BiocCheck('curatedPCaData_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 7 minutes 5.31 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 3948.12 KiB |
| BuildID:: curatedPCaData_20230530130915 |
| 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. Checking Package status: 1. |
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_0.99.0.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('curatedPCaData')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: curatedPCaData
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3047/curatedPCaData_20230530130915/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/curatedPCaData_20230530130915/curatedPCaData.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 ‘curatedPCaData/DESCRIPTION’ ... OK
* this is package ‘curatedPCaData’ version ‘0.99.0’
* 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 ... [9s/9s] 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 ... [33s/33s] 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 ... [179s/203s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
curatedPCaDatasets_abida 12.958 0.765 15.321
curatedPCaDatasets_tcga 9.361 0.540 11.267
getPCa 9.481 0.356 11.331
curatedPCaDatasets_taylor 9.396 0.256 11.039
curatedPCaDatasets_barbieri 8.570 0.204 10.217
curatedPCaDatasets_ren 8.226 0.435 9.963
curatedPCaDatasets_weiner 8.182 0.264 9.571
curatedPCaDatasets_chandran 7.493 0.231 8.837
curatedPCaDatasets_friedrich 7.264 0.196 8.724
curatedPCaDatasets_kunderfranco 7.337 0.077 8.540
curatedPCaDatasets_kim 7.228 0.179 8.925
curatedPCaDatasets_sun 7.180 0.176 8.471
curatedPCaDatasets_icgcca 7.149 0.104 8.500
curatedPCaDatasets_wang 7.044 0.144 8.328
curatedPCaDatasets_wallace 6.959 0.193 8.256
curatedPCaDatasets_igc 6.989 0.136 8.259
curatedPCaDatasets_true 6.554 0.376 7.988
curatedPCaDatasets_barwick 5.558 0.109 6.559
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [10s/10s]
[10s/10s] ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 20 lines of output:
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
Error in library("RUnit", quietly = TRUE) :
there is no package called 'RUnit'
Calls: <Anonymous> -> library
Execution halted
* 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 ... [3s/3s] OK
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3047/curatedPCaData_20230530130915/curatedPCaData.Rcheck/00check.log’
for details.
===============================
BiocCheck('curatedPCaData_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: curatedPCaData
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/RtmpLq8sZZ/file11a40f445ba703/curatedPCaData
─ installDir: /tmp/RtmpLq8sZZ/file11a40f6a5997f9
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3047/curatedPCaData_20230530130915/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; 640 lines (21%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 589 lines
(19%) 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: 0.99.0 |
| 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: 5 minutes 58.33 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/curatedPCaData_20230530130915/curatedPCaData.install-out.txt curatedPCaData_0.99.0.tar.gz && BiocCheck('curatedPCaData_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 5 minutes 47.35 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh curatedPCaData_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 30.84 seconds |
| PackageFileSize: 4071.61 KiB |
| BuildID:: curatedPCaData_20230530130915 |
| 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. Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
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_0.99.0.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('curatedPCaData')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: curatedPCaData
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3047/curatedPCaData_20230530130915/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/curatedPCaData_20230530130915/curatedPCaData.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 ‘curatedPCaData/DESCRIPTION’ ... OK
* this is package ‘curatedPCaData’ version ‘0.99.0’
* 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [24s/24s] 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 ... [139s/162s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
curatedPCaDatasets_abida 10.379 0.993 13.100
curatedPCaDatasets_barbieri 6.998 0.542 8.922
getPCa 6.940 0.517 9.103
curatedPCaDatasets_taylor 6.834 0.543 8.765
curatedPCaDatasets_tcga 6.705 0.512 8.547
curatedPCaDatasets_ren 6.058 0.439 7.949
curatedPCaDatasets_weiner 5.772 0.465 7.416
curatedPCaDatasets_chandran 5.764 0.410 7.295
curatedPCaDatasets_friedrich 5.461 0.429 7.039
curatedPCaDatasets_icgcca 5.429 0.416 6.963
curatedPCaDatasets_kim 5.433 0.381 6.906
curatedPCaDatasets_sun 5.261 0.438 6.878
curatedPCaDatasets_igc 5.253 0.388 6.774
curatedPCaDatasets_kunderfranco 5.248 0.392 6.817
curatedPCaDatasets_wallace 5.203 0.417 6.782
curatedPCaDatasets_wang 5.175 0.410 6.958
curatedPCaDatasets_true 4.694 0.364 6.185
curatedPCaDatasets_barwick 4.198 0.323 5.527
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [25s/28s]
[25s/28s] 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 ... [5s/5s] OK
* DONE
Status: OK
===============================
BiocCheck('curatedPCaData_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: curatedPCaData
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpUiXQaM/filebcfa356385a/curatedPCaData
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpUiXQaM/filebcfa689bcd74
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3047/curatedPCaData_20230530130915/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; 640 lines (21%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 589 lines
(19%) 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_0.99.0.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)