merida1 Summary
[top]
Package: seq.hotSPOT |
Version: 0.99.1 |
RVersion: 4.3
|
BiocVersion: 3.17
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data seq.hotSPOT |
BuildTime: 0 minutes 11.47 seconds |
CheckCommand: BiocCheckGitClone('seq.hotSPOT') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2922/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2922/ef7e86d2a6e59018353a4b273c77ba3dc1c8281a/seq.hotSPOT.install-out.txt seq.hotSPOT_0.99.1.tar.gz && BiocCheck('seq.hotSPOT_0.99.1.tar.gz', `new-package`=TRUE) |
CheckTime: 0 minutes 32.67 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh seq.hotSPOT_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 2.73 seconds |
PackageFileSize: 19.55 KiB |
BuildID:: seq.hotSPOT_20230324181550 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: seq.hotSPOT. 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 ‘seq.hotSPOT/DESCRIPTION’ ... OK
* preparing ‘seq.hotSPOT’:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘seq.hotSPOT/data/mutation_data.RData’
* building ‘seq.hotSPOT_0.99.1.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('seq.hotSPOT')
===============================
─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: seq.hotSPOT
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2922/ef7e86d2a6e59018353a4b273c77ba3dc1c8281a/seq.hotSPOT
─ 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/2922/ef7e86d2a6e59018353a4b273c77ba3dc1c8281a/seq.hotSPOT.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* 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 ‘seq.hotSPOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seq.hotSPOT’ version ‘0.99.1’
* 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 ‘seq.hotSPOT’ 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 ... [4s/4s] NOTE
amp_pool: no visible global function definition for ‘ftable’
amp_pool: no visible binding for global variable ‘chr’
com_hotspot: no visible global function definition for ‘ftable’
com_hotspot: no visible binding for global variable ‘id’
com_hotspot: no visible global function definition for ‘median’
fw_hotspot: no visible global function definition for ‘ftable’
fw_hotspot: no visible binding for global variable ‘id’
fw_hotspot: no visible binding for global variable ‘count’
Undefined global functions or variables:
chr count ftable id median
Consider adding
importFrom("stats", "ftable", "median")
to your NAMESPACE file.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
com_hotspot 6.843 0.015 6.857
* 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
‘/Users/pkgbuild/packagebuilder/workers/jobs/2922/ef7e86d2a6e59018353a4b273c77ba3dc1c8281a/seq.hotSPOT.Rcheck/00check.log’
for details.
===============================
BiocCheck('seq.hotSPOT_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: seq.hotSPOT
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpQHUkp5/file6a966f2ae09d/seq.hotSPOT
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpQHUkp5/file6a961e70c1
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2922/ef7e86d2a6e59018353a4b273c77ba3dc1c8281a/seq.hotSPOT.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 3.5.0 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* 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...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of seq.hotSPOT...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 4 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 135 lines (12%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 117 lines (10%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 370 lines
(32%) 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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 12 NOTES
See the seq.hotSPOT.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 seq.hotSPOT_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘seq.hotSPOT’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (seq.hotSPOT)
nebbiolo1 Summary
[top]
Package: seq.hotSPOT |
Version: 0.99.1 |
RVersion: 4.3
|
BiocVersion: 3.17
|
BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data seq.hotSPOT |
BuildTime: 0 minutes 9.50 seconds |
CheckCommand: BiocCheckGitClone('seq.hotSPOT') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2922/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2922/ef7e86d2a6e59018353a4b273c77ba3dc1c8281a/seq.hotSPOT.install-out.txt seq.hotSPOT_0.99.1.tar.gz && BiocCheck('seq.hotSPOT_0.99.1.tar.gz', `new-package`=TRUE) |
CheckTime: 0 minutes 27.96 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 19.55 KiB |
BuildID:: seq.hotSPOT_20230324181550 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: seq.hotSPOT. 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
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘seq.hotSPOT/DESCRIPTION’ ... OK
* preparing ‘seq.hotSPOT’:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘seq.hotSPOT/data/mutation_data.RData’
* building ‘seq.hotSPOT_0.99.1.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('seq.hotSPOT')
===============================
─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: seq.hotSPOT
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2922/ef7e86d2a6e59018353a4b273c77ba3dc1c8281a/seq.hotSPOT
─ 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/2922/ef7e86d2a6e59018353a4b273c77ba3dc1c8281a/seq.hotSPOT.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* 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 ‘seq.hotSPOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seq.hotSPOT’ version ‘0.99.1’
* 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 ‘seq.hotSPOT’ 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 ... [4s/4s] NOTE
amp_pool: no visible global function definition for ‘ftable’
amp_pool: no visible binding for global variable ‘chr’
com_hotspot: no visible global function definition for ‘ftable’
com_hotspot: no visible binding for global variable ‘id’
com_hotspot: no visible global function definition for ‘median’
fw_hotspot: no visible global function definition for ‘ftable’
fw_hotspot: no visible binding for global variable ‘id’
fw_hotspot: no visible binding for global variable ‘count’
Undefined global functions or variables:
chr count ftable id median
Consider adding
importFrom("stats", "ftable", "median")
to your NAMESPACE file.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
com_hotspot 5.734 0.004 5.738
* 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 ... [2s/2s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2922/ef7e86d2a6e59018353a4b273c77ba3dc1c8281a/seq.hotSPOT.Rcheck/00check.log’
for details.
===============================
BiocCheck('seq.hotSPOT_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: seq.hotSPOT
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/RtmprZi2m9/file392732284dd306/seq.hotSPOT
─ installDir: /tmp/RtmprZi2m9/file3927327ced31b1
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2922/ef7e86d2a6e59018353a4b273c77ba3dc1c8281a/seq.hotSPOT.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 3.5.0 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* 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...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of seq.hotSPOT...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 4 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 135 lines (12%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 117 lines (10%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 370 lines
(32%) 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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 12 NOTES
See the seq.hotSPOT.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]