nebbiolo2 Summary
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| Package: GenomicPlot |
| Version: 0.99.15 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicPlot |
| BuildTime: 2 minutes 10.90 seconds |
| CheckCommand: BiocCheckGitClone('GenomicPlot') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3046/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3046/c03036c284af9589195af1550c2598446225146d/GenomicPlot.install-out.txt GenomicPlot_0.99.15.tar.gz && BiocCheck('GenomicPlot_0.99.15.tar.gz', `new-package`=TRUE) |
| CheckTime: 9 minutes 55.39 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2899.19 KiB |
| BuildID:: GenomicPlot_20230728123047 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: GenomicPlot. 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. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘GenomicPlot/DESCRIPTION’ ... OK
* preparing ‘GenomicPlot’:
* 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 ‘GenomicPlot_0.99.15.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('GenomicPlot')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: GenomicPlot
─ PackageVersion: 0.99.15
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3046/c03036c284af9589195af1550c2598446225146d/GenomicPlot
─ 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/3046/c03036c284af9589195af1550c2598446225146d/GenomicPlot.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 ‘GenomicPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicPlot’ version ‘0.99.15’
* 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 ‘GenomicPlot’ 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 ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/14s] OK
* checking loading without being on the library search path ... [14s/14s] 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 ... [50s/50s] NOTE
get_targeted_genes: no visible binding for global variable ‘5'UTR’
get_targeted_genes: no visible binding for global variable ‘3'UTR’
plot_bam_correlation: no visible binding for global variable ‘.’
plot_peak_annotation: no visible binding for global variable ‘.’
Undefined global functions or variables:
. 3'UTR 5'UTR
* 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 ... [3s/3s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [191s/178s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_start_end_with_random 14.046 3.020 15.902
plot_region 12.886 2.941 11.664
plot_locus 12.117 2.015 11.724
plot_5parts_metagene 9.781 2.508 9.403
plot_locus_with_random 8.861 1.878 8.447
plot_start_end 8.692 1.843 9.834
plot_peak_annotation 6.999 0.015 7.014
get_targeted_genes 5.319 0.123 5.443
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-plotFunctions.R’ [120s/103s]
Running ‘test-shortFunctions.R’ [21s/20s]
[141s/123s] 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3046/c03036c284af9589195af1550c2598446225146d/GenomicPlot.Rcheck/00check.log’
for details.
===============================
BiocCheck('GenomicPlot_0.99.15.tar.gz')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: GenomicPlot
─ PackageVersion: 0.99.15
─ sourceDir: /tmp/RtmpddhwLw/file12201443d7f33c/GenomicPlot
─ installDir: /tmp/RtmpddhwLw/file12201424b038ca
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3046/c03036c284af9589195af1550c2598446225146d/GenomicPlot.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...
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 GenomicPlot...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 25 functions greater than 50 lines.
* Checking man page documentation...
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* 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; 99 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1326 lines
(10%) 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 | 7 NOTES
See the GenomicPlot.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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lconway Summary
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| Package: GenomicPlot |
| Version: 0.99.15 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicPlot |
| BuildTime: 1 minutes 38.16 seconds |
| CheckCommand: BiocCheckGitClone('GenomicPlot') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3046/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3046/c03036c284af9589195af1550c2598446225146d/GenomicPlot.install-out.txt GenomicPlot_0.99.15.tar.gz && BiocCheck('GenomicPlot_0.99.15.tar.gz', `new-package`=TRUE) |
| CheckTime: 7 minutes 1.72 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh GenomicPlot_0.99.15.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 33.10 seconds |
| PackageFileSize: 3194.74 KiB |
| BuildID:: GenomicPlot_20230728123047 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: GenomicPlot. 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. Adding Build Product Information to Database.Checking Package status: 1. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘GenomicPlot/DESCRIPTION’ ... OK
* preparing ‘GenomicPlot’:
* 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 ‘GenomicPlot_0.99.15.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('GenomicPlot')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: GenomicPlot
─ PackageVersion: 0.99.15
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3046/c03036c284af9589195af1550c2598446225146d/GenomicPlot
─ 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/3046/c03036c284af9589195af1550c2598446225146d/GenomicPlot.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 ‘GenomicPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicPlot’ version ‘0.99.15’
* 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 ‘GenomicPlot’ 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [36s/36s] NOTE
get_targeted_genes: no visible binding for global variable ‘5'UTR’
get_targeted_genes: no visible binding for global variable ‘3'UTR’
plot_bam_correlation: no visible binding for global variable ‘.’
plot_peak_annotation: no visible binding for global variable ‘.’
Undefined global functions or variables:
. 3'UTR 5'UTR
* 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 ... [2s/2s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [145s/130s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_region 9.552 3.558 8.862
plot_start_end_with_random 9.506 2.820 10.121
plot_locus 8.842 2.294 8.543
plot_5parts_metagene 6.874 2.692 6.884
plot_locus_with_random 6.642 2.331 6.495
plot_start_end 5.949 1.401 6.326
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-plotFunctions.R’ [79s/63s]
Running ‘test-shortFunctions.R’ [14s/14s]
[93s/78s] ERROR
Running the tests in ‘tests/test-plotFunctions.R’ failed.
Last 20 lines of output:
2. └─GenomicPlot::process_scoreMatrix(...)
3. └─GenomicPlot:::impute_hm(fullmatrix, verbose)
── Warning (???): testing plot_start_end_with_random ───────────────────────────
no non-missing arguments to min; returning Inf
Backtrace:
▆
1. └─GenomicPlot::plot_start_end_with_random(...)
2. └─GenomicPlot::process_scoreMatrix(...)
3. └─GenomicPlot:::impute_hm(fullmatrix, verbose)
── Error (???): testing plot_start_end_with_random ─────────────────────────────
Error in `smooth.spline(rsub_df$Intensity, df = as.integer(bin_num/5))`: missing or infinite values in inputs are not allowed
Backtrace:
▆
1. └─GenomicPlot::plot_start_end_with_random(...)
2. ├─base::as.vector(smooth.spline(rsub_df$Intensity, df = as.integer(bin_num/5))$y)
3. └─stats::smooth.spline(rsub_df$Intensity, df = as.integer(bin_num/5))
Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
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 ... [5s/5s] OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3046/c03036c284af9589195af1550c2598446225146d/GenomicPlot.Rcheck/00check.log’
for details.
===============================
BiocCheck('GenomicPlot_0.99.15.tar.gz')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: GenomicPlot
─ PackageVersion: 0.99.15
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpTkZeuu/file63bb39dd8022/GenomicPlot
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpTkZeuu/file63bb6c95dcfd
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3046/c03036c284af9589195af1550c2598446225146d/GenomicPlot.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...
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 GenomicPlot...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 25 functions greater than 50 lines.
* Checking man page documentation...
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* 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; 99 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1326 lines
(10%) 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 | 7 NOTES
See the GenomicPlot.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 GenomicPlot_0.99.15.tar.gz'
>>>>>>>
* installing *source* package ‘GenomicPlot’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicPlot)