Bioconductor Single Package Builder - Build History
nebbiolo1 Summary
| Package: DifferentialRegulation |
| Version: 0.99.6 |
| RVersion: 4.2 |
| BiocVersion: 3.15 |
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DifferentialRegulation |
| BuildTime: 1 minutes 12.30 seconds |
| CheckCommand: BiocCheckGitClone('DifferentialRegulation') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings DifferentialRegulation_0.99.6.tar.gz && BiocCheck('DifferentialRegulation_0.99.6.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 8.17 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 579.25 KiB |
| BuildID:: DifferentialRegulation_20220421122818 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DifferentialRegulation. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
=============================== R CMD BUILD =============================== * checking for file ‘DifferentialRegulation/DESCRIPTION’ ... OK * preparing ‘DifferentialRegulation’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to process help pages * saving partial Rd database * creating vignettes ... OK * cleaning src * 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 ‘DifferentialRegulation_0.99.6.tar.gz’
nebbiolo1 CHECK output
===============================
BiocCheckGitClone('DifferentialRegulation')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: DifferentialRegulation
─ PackageVersion: 0.99.6
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2611/8680176e689097db0d8c09148951998262ec3f67/DifferentialRegulation
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be git tracked.
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2611/8680176e689097db0d8c09148951998262ec3f67/DifferentialRegulation.Rcheck’
* using R version 4.2.0 beta (2022-04-12 r82161)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DifferentialRegulation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DifferentialRegulation’ version ‘0.99.6’
* 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 ‘DifferentialRegulation’ can be installed ... [36s/36s] 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [17s/17s] 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/22s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DifferentialRegulation 0.945 0.046 13.212
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testhat.R’ [8s/20s]
[8s/20s] 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 ... OK
* DONE
Status: OK
===============================
BiocCheck('DifferentialRegulation_0.99.6.tar.gz')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: DifferentialRegulation
─ PackageVersion: 0.99.6
─ sourceDir: /tmp/RtmpxIWVTR/file14faeb9741b08/DifferentialRegulation
─ installDir: /tmp/RtmpxIWVTR/file14faeb5d950b44
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2611/8680176e689097db0d8c09148951998262ec3f67/DifferentialRegulation.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 4.1.0 to 4.2.0.
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
ATACSeq
Search 'biocViews' at https://contributions.bioconductor.org
* 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 DifferentialRegulation...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 5
functions > 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; 304 lines (15%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 944 lines
(46%) are not.
See http://bioconductor.org/developers/how-to/coding-style/
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 | 6 NOTES
See the DifferentialRegulation.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
merida1 Summary
| Package: DifferentialRegulation |
| Version: 0.99.6 |
| RVersion: 4.2 |
| BiocVersion: 3.15 |
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DifferentialRegulation |
| BuildTime: 3 minutes 39.77 seconds |
| CheckCommand: BiocCheckGitClone('DifferentialRegulation') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DifferentialRegulation_0.99.6.tar.gz && BiocCheck('DifferentialRegulation_0.99.6.tar.gz', `new-package`=TRUE) |
| CheckTime: 11 minutes 12.46 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh DifferentialRegulation_0.99.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 2 minutes 25.96 seconds |
| PackageFileSize: 1159.07 KiB |
| BuildID:: DifferentialRegulation_20220421122818 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DifferentialRegulation. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
=============================== R CMD BUILD =============================== * checking for file ‘DifferentialRegulation/DESCRIPTION’ ... OK * preparing ‘DifferentialRegulation’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to process help pages * saving partial Rd database * creating vignettes ... OK * cleaning src * 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 ‘DifferentialRegulation_0.99.6.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/Bioconductor_installation_aafc17897df6131e0feea75fd5c1861d.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/Bioconductor_installation_aafc17897df6131e0feea75fd5c1861d.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/Bioconductor_installation_aafc17897df6131e0feea75fd5c1861d.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/EC-test_34f362f5844b0ccee54277060266f1cd.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/EC-test_34f362f5844b0ccee54277060266f1cd.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/EC-test_34f362f5844b0ccee54277060266f1cd.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/cell-type_c7ecea9a776e10deab76a8e24bc16db1.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/cell-type_c7ecea9a776e10deab76a8e24bc16db1.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/cell-type_c7ecea9a776e10deab76a8e24bc16db1.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/citation_1fb283b1c6e2a35acc58521feac7971a.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/citation_1fb283b1c6e2a35acc58521feac7971a.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/citation_1fb283b1c6e2a35acc58521feac7971a.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/load_380c823ac2ab15f177dbdab20c2467d6.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/load_380c823ac2ab15f177dbdab20c2467d6.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/load_380c823ac2ab15f177dbdab20c2467d6.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/load_EC_counts_ff9e48fc7895655babc3fe9af9d7acbd.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/load_EC_counts_ff9e48fc7895655babc3fe9af9d7acbd.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/load_EC_counts_ff9e48fc7895655babc3fe9af9d7acbd.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/load_USA_counts_fe2bff7964c9d2ba2b897fa27592d6ed.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/load_USA_counts_fe2bff7964c9d2ba2b897fa27592d6ed.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/load_USA_counts_fe2bff7964c9d2ba2b897fa27592d6ed.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/samples_design_e7a59a7f0387df98acfd6731cff89027.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/samples_design_e7a59a7f0387df98acfd6731cff89027.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/samples_design_e7a59a7f0387df98acfd6731cff89027.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/sce-test_9ae1c069f95f5f5f5342d04c0be4fd76.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/sce-test_9ae1c069f95f5f5f5342d04c0be4fd76.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/sce-test_9ae1c069f95f5f5f5342d04c0be4fd76.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/sce_assays_da5ed38f1c29e81bfb2462853e942117.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/sce_assays_da5ed38f1c29e81bfb2462853e942117.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/sce_assays_da5ed38f1c29e81bfb2462853e942117.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/sessionInfo_b6fb6cfc225315d96d7492791bc6482d.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/sessionInfo_b6fb6cfc225315d96d7492791bc6482d.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/sessionInfo_b6fb6cfc225315d96d7492791bc6482d.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/specify_data-dir_2b3415c4613cea8bd45a2a448c7e8eb1.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/specify_data-dir_2b3415c4613cea8bd45a2a448c7e8eb1.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/specify_data-dir_2b3415c4613cea8bd45a2a448c7e8eb1.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/specify_directories_EC_62902065e4f63d6275ca8ac325ccbfcc.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/specify_directories_EC_62902065e4f63d6275ca8ac325ccbfcc.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/specify_directories_EC_62902065e4f63d6275ca8ac325ccbfcc.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/specify_directories_cb18a80a3775af83b883e1eb0fd82932.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/specify_directories_cb18a80a3775af83b883e1eb0fd82932.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/specify_directories_cb18a80a3775af83b883e1eb0fd82932.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/vignettes_6db9b63e7676a1b905fcbfa4e34b23f0.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/vignettes_6db9b63e7676a1b905fcbfa4e34b23f0.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/vignettes_6db9b63e7676a1b905fcbfa4e34b23f0.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/visualize_results_EC_c6d54a4fa751abef7cc5df7eb5929520.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/visualize_results_EC_c6d54a4fa751abef7cc5df7eb5929520.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/visualize_results_EC_c6d54a4fa751abef7cc5df7eb5929520.rdx’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/visualize_results_USA_6d74427018ebe30c041e1be8e7c498c2.RData’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/visualize_results_USA_6d74427018ebe30c041e1be8e7c498c2.rdb’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘DifferentialRegulation/vignettes/DifferentialRegulation_cache/html/visualize_results_USA_6d74427018ebe30c041e1be8e7c498c2.rdx’
merida1 CHECK output
===============================
BiocCheckGitClone('DifferentialRegulation')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: DifferentialRegulation
─ PackageVersion: 0.99.6
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2611/8680176e689097db0d8c09148951998262ec3f67/DifferentialRegulation
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be git tracked.
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2611/8680176e689097db0d8c09148951998262ec3f67/DifferentialRegulation.Rcheck’
* using R version 4.2.0 beta (2022-04-12 r82161)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DifferentialRegulation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DifferentialRegulation’ version ‘0.99.6’
* 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 ... NOTE
Found the following non-portable file paths:
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Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DifferentialRegulation’ can be installed ... [105s/114s] 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [55s/58s] 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [28s/89s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DifferentialRegulation 3.842 0.281 62.281
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testhat.R’ [30s/87s]
[30s/87s] 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 ... OK
* DONE
Status: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2611/8680176e689097db0d8c09148951998262ec3f67/DifferentialRegulation.Rcheck/00check.log’
for details.
===============================
BiocCheck('DifferentialRegulation_0.99.6.tar.gz')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: DifferentialRegulation
─ PackageVersion: 0.99.6
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpBC5ltq/file127df6989245d/DifferentialRegulation
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpBC5ltq/file127df2ff813fa
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2611/8680176e689097db0d8c09148951998262ec3f67/DifferentialRegulation.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 4.1.0 to 4.2.0.
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
ATACSeq
Search 'biocViews' at https://contributions.bioconductor.org
* 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 DifferentialRegulation...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 5
functions > 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; 304 lines (15%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 944 lines
(46%) are not.
See http://bioconductor.org/developers/how-to/coding-style/
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 | 6 NOTES
See the DifferentialRegulation.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
=============================== R CMD BUILD =============================== >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir DifferentialRegulation_0.99.6.tar.gz' >>>>>>> * installing *source* package ‘DifferentialRegulation’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Rcpp_MCMC.cpp -o Rcpp_MCMC.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Rcpp_MCMC_sce.cpp -o Rcpp_MCMC_sce.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DifferentialRegulation.so RcppExports.o Rcpp_MCMC.o Rcpp_MCMC_sce.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/pkgbuild/packagebuilder/workers/jobs/2611/8680176e689097db0d8c09148951998262ec3f67/libdir/00LOCK-DifferentialRegulation/00new/DifferentialRegulation/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DifferentialRegulation) >>>>>>> >>>>>>> FIXING LINKS FOR libdir/DifferentialRegulation/libs/DifferentialRegulation.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "libdir/DifferentialRegulation/libs/DifferentialRegulation.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/DifferentialRegulation/libs/DifferentialRegulation.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/DifferentialRegulation/libs/DifferentialRegulation.so" install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/DifferentialRegulation/libs/DifferentialRegulation.so" install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/DifferentialRegulation/libs/DifferentialRegulation.so"