nebbiolo1 Summary
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| Package: LipidSigR |
| Version: 0.99.12 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data LipidSigR |
| BuildTime: 4 minutes 48.70 seconds |
| CheckCommand: BiocCheckGitClone('LipidSigR') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2631/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2631/57893c4761b908b08d85594b418eaa6669cad82e/LipidSigR.install-out.txt LipidSigR_0.99.12.tar.gz && BiocCheck('LipidSigR_0.99.12.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 9.92 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4693.80 KiB |
| BuildID:: LipidSigR_20230116032114 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: LipidSigR. 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. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘LipidSigR/DESCRIPTION’ ... OK
* preparing ‘LipidSigR’:
* 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 ‘LipidSigR_0.99.12.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('LipidSigR')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: LipidSigR
─ PackageVersion: 0.99.12
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2631/57893c4761b908b08d85594b418eaa6669cad82e/LipidSigR
─ 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...
─ 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/2631/57893c4761b908b08d85594b418eaa6669cad82e/LipidSigR.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* 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 22.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LipidSigR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LipidSigR’ version ‘0.99.12’
* 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 ‘LipidSigR’ 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [13s/13s] 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 files in ‘vignettes’ ... OK
* checking examples ... [112s/101s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ML_final 6.848 0.851 6.937
SHAP 4.759 1.183 4.704
SHAP_dependence_plot 4.652 1.128 4.508
SHAP_forceplot 4.529 1.074 4.359
pathview_function 5.346 0.234 5.582
SHAP_sample 4.439 1.078 4.363
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [146s/96s]
[146s/97s] 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] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character ∂ (U+2202)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
* checking PDF version of manual without index ... ERROR
* DONE
Status: 1 ERROR, 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2631/57893c4761b908b08d85594b418eaa6669cad82e/LipidSigR.Rcheck/00check.log’
for details.
===============================
BiocCheck('LipidSigR_0.99.12.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: LipidSigR
─ PackageVersion: 0.99.12
─ sourceDir: /tmp/RtmphyUJ9u/file23371c71b90127/LipidSigR
─ installDir: /tmp/RtmphyUJ9u/file23371c1826e621
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2631/57893c4761b908b08d85594b418eaa6669cad82e/LipidSigR.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 4.0.0 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 LipidSigR...
* 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 89 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; 50 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 5791 lines
(35%) 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 | 4 NOTES
See the LipidSigR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: LipidSigR |
| Version: 0.99.12 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data LipidSigR |
| BuildTime: 8 minutes 51.66 seconds |
| CheckCommand: BiocCheckGitClone('LipidSigR') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2631/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2631/57893c4761b908b08d85594b418eaa6669cad82e/LipidSigR.install-out.txt LipidSigR_0.99.12.tar.gz && BiocCheck('LipidSigR_0.99.12.tar.gz', `new-package`=TRUE) |
| CheckTime: 7 minutes 56.02 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh LipidSigR_0.99.12.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 21.59 seconds |
| PackageFileSize: 4686.30 KiB |
| BuildID:: LipidSigR_20230116032114 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: LipidSigR. 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. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘LipidSigR/DESCRIPTION’ ... OK
* preparing ‘LipidSigR’:
* 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 ‘LipidSigR_0.99.12.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('LipidSigR')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: LipidSigR
─ PackageVersion: 0.99.12
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2631/57893c4761b908b08d85594b418eaa6669cad82e/LipidSigR
─ 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...
─ 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/2631/57893c4761b908b08d85594b418eaa6669cad82e/LipidSigR.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LipidSigR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LipidSigR’ version ‘0.99.12’
* 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 ‘LipidSigR’ 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [32s/35s] OK
* checking Rd files ... [1s/2s] 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 ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [185s/180s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ML_final 10.445 1.176 11.097
pathview_function 10.489 0.673 12.464
SHAP 7.703 1.495 7.435
SHAP_forceplot 7.564 1.463 7.298
SHAP_dependence_plot 7.466 1.519 7.177
SHAP_sample 7.417 1.475 7.135
probability_plot 6.645 0.930 6.682
Clin_Cor_heatmap 7.236 0.274 8.399
PR_plot_all 5.972 1.213 5.988
ROC_plot_all 6.077 1.026 6.110
Hclustering 6.927 0.088 7.829
cor_network 5.957 0.977 5.866
feature_plot 5.787 0.952 5.637
evalution_plot 5.630 0.907 5.475
model_for_net 5.396 1.002 5.136
DE_sub_char_plot_2 6.024 0.150 6.938
Clin_LR_heatmap 4.634 0.112 5.289
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [215s/167s]
[215s/167s] 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 ... [19s/21s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode character ∂ (U+2202)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
* checking PDF version of manual without index ... ERROR
* DONE
Status: 1 ERROR, 1 WARNING
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2631/57893c4761b908b08d85594b418eaa6669cad82e/LipidSigR.Rcheck/00check.log’
for details.
===============================
BiocCheck('LipidSigR_0.99.12.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: LipidSigR
─ PackageVersion: 0.99.12
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpxyK4EF/file16ce54b7d6877/LipidSigR
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpxyK4EF/file16ce548225383
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2631/57893c4761b908b08d85594b418eaa6669cad82e/LipidSigR.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 4.0.0 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 LipidSigR...
* 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 89 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; 50 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 5791 lines
(35%) 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 | 4 NOTES
See the LipidSigR.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 LipidSigR_0.99.12.tar.gz'
>>>>>>>
* installing *source* package ‘LipidSigR’ ...
** 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 (LipidSigR)