lconway Summary
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Package: nipalsMCIA |
Version: 0.99.4 |
RVersion: 4.3
|
BiocVersion: 3.18
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data nipalsMCIA |
BuildTime: 3 minutes 14.80 seconds |
CheckCommand: BiocCheckGitClone('nipalsMCIA') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2914/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2914/d4e67bc7154b5b1f35d9189f8b95f351291f0341/nipalsMCIA.install-out.txt nipalsMCIA_0.99.4.tar.gz && BiocCheck('nipalsMCIA_0.99.4.tar.gz', `new-package`=TRUE) |
CheckTime: 4 minutes 22.07 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh nipalsMCIA_0.99.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 24.78 seconds |
PackageFileSize: 3597.09 KiB |
BuildID:: nipalsMCIA_20230602022226 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: nipalsMCIA. 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: 1. Build Package status: 0. |
lconway BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* preparing ‘nipalsMCIA’:
* 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 ‘nipalsMCIA_0.99.4.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('nipalsMCIA')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: nipalsMCIA
─ PackageVersion: 0.99.4
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2914/d4e67bc7154b5b1f35d9189f8b95f351291f0341/nipalsMCIA
─ 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/2914/d4e67bc7154b5b1f35d9189f8b95f351291f0341/nipalsMCIA.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 ‘nipalsMCIA/DESCRIPTION’ ... OK
* this is package ‘nipalsMCIA’ version ‘0.99.4’
* 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 ‘nipalsMCIA’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [25s/25s] 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 files in ‘vignettes’ ... OK
* checking examples ... [62s/63s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
nipals_multiblock 4.767 0.576 5.348
global_scores_eigenvalues_plot 4.356 0.720 5.087
block_weights_heatmap 4.529 0.503 5.036
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [27s/28s]
[27s/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 ... [6s/6s] OK
* DONE
Status: OK
===============================
BiocCheck('nipalsMCIA_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: nipalsMCIA
─ PackageVersion: 0.99.4
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp5kaaj9/file292d38a49860/nipalsMCIA
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp5kaaj9/file292d52c92b0
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2914/d4e67bc7154b5b1f35d9189f8b95f351291f0341/nipalsMCIA.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
Error in `[.data.frame`(pkg_status, , "PackageStatus") :
undefined columns selected
Calls: BiocCheck ... getAllDeprecatedPkgs -> get_deprecated_status -> [ -> [.data.frame
Execution halted
lconway BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir nipalsMCIA_0.99.4.tar.gz'
>>>>>>>
* installing *source* package ‘nipalsMCIA’ ...
** 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 (nipalsMCIA)
nebbiolo2 Summary
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Package: nipalsMCIA |
Version: 0.99.4 |
RVersion: 4.3
|
BiocVersion: 3.18
|
BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data nipalsMCIA |
BuildTime: 3 minutes 14.22 seconds |
CheckCommand: BiocCheckGitClone('nipalsMCIA') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2914/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2914/d4e67bc7154b5b1f35d9189f8b95f351291f0341/nipalsMCIA.install-out.txt nipalsMCIA_0.99.4.tar.gz && BiocCheck('nipalsMCIA_0.99.4.tar.gz', `new-package`=TRUE) |
CheckTime: 4 minutes 32.38 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 3576.76 KiB |
BuildID:: nipalsMCIA_20230602022226 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: nipalsMCIA. 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: 1. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* preparing ‘nipalsMCIA’:
* 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 ‘nipalsMCIA_0.99.4.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('nipalsMCIA')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: nipalsMCIA
─ PackageVersion: 0.99.4
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2914/d4e67bc7154b5b1f35d9189f8b95f351291f0341/nipalsMCIA
─ 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/2914/d4e67bc7154b5b1f35d9189f8b95f351291f0341/nipalsMCIA.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 ‘nipalsMCIA/DESCRIPTION’ ... OK
* this is package ‘nipalsMCIA’ version ‘0.99.4’
* 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 ‘nipalsMCIA’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [63s/63s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
nipals_multiblock 5.235 0.068 5.304
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [33s/33s]
[33s/34s] 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 ... [3s/3s] OK
* DONE
Status: OK
===============================
BiocCheck('nipalsMCIA_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: nipalsMCIA
─ PackageVersion: 0.99.4
─ sourceDir: /tmp/RtmpAgiBQM/file16281615cd0a43/nipalsMCIA
─ installDir: /tmp/RtmpAgiBQM/file16281627163f26
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2914/d4e67bc7154b5b1f35d9189f8b95f351291f0341/nipalsMCIA.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
Error in `[.data.frame`(pkg_status, , "PackageStatus") :
undefined columns selected
Calls: BiocCheck ... getAllDeprecatedPkgs -> get_deprecated_status -> [ -> [.data.frame
Execution halted
nebbiolo2 BUILD BIN output
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