nebbiolo2 Summary
[top]
| Package: MICSQTL |
| Version: 0.99.2 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MICSQTL |
| BuildTime: 11 minutes 40.57 seconds |
| CheckCommand: BiocCheckGitClone('MICSQTL') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3023/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3023/MICSQTL_20230530124852/MICSQTL.install-out.txt MICSQTL_0.99.2.tar.gz && BiocCheck('MICSQTL_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 8.27 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 3737.70 KiB |
| BuildID:: MICSQTL_20230530124852 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MICSQTL. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘MICSQTL/DESCRIPTION’ ... OK
* preparing ‘MICSQTL’:
* 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 ‘MICSQTL_0.99.2.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('MICSQTL')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: MICSQTL
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3023/MICSQTL_20230530124852/MICSQTL
─ 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/3023/MICSQTL_20230530124852/MICSQTL.Rcheck’
* using R version 4.3.0 RC (2023-04-18 r84287)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MICSQTL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MICSQTL’ version ‘0.99.2’
* 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 ‘MICSQTL’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [24s/24s] 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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] ERROR
Running examples in ‘MICSQTL-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TCA_deconv
> ### Title: Estimation of cellular expression in high-throughput data from
> ### heterogeneous tissues
> ### Aliases: TCA_deconv
>
> ### ** Examples
>
> data(se)
> se <- deconv(se, source = "protein", method = "cibersort")
Error in .check_ncores(cores) : 3 simultaneous processes spawned
Calls: deconv -> CIBERSORT -> CoreAlg -> mclapply -> .check_ncores
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [13s/12s]
[13s/12s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character ≥ (U+2265)
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: 2 ERRORs, 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3023/MICSQTL_20230530124852/MICSQTL.Rcheck/00check.log’
for details.
===============================
BiocCheck('MICSQTL_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: MICSQTL
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/RtmpbTQCcj/file1189794e1cafd3/MICSQTL
─ installDir: /tmp/RtmpbTQCcj/file1189792f764203
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3023/MICSQTL_20230530124852/MICSQTL.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 4.2.0 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...
* NOTE: Consider adding these automatically suggested biocViews:
Coverage
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...
* 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...
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
* 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 MICSQTL...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 7 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* 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; 26 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 75 lines
(3%) 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...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/
─ BiocCheck results ──
2 ERRORS | 1 WARNINGS | 8 NOTES
See the MICSQTL.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]
lconway Summary
[top]
| Package: MICSQTL |
| Version: 0.99.2 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MICSQTL |
| BuildTime: 6 minutes 34.33 seconds |
| CheckCommand: BiocCheckGitClone('MICSQTL') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3023/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3023/MICSQTL_20230530124852/MICSQTL.install-out.txt MICSQTL_0.99.2.tar.gz && BiocCheck('MICSQTL_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 23.84 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh MICSQTL_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 17.27 seconds |
| PackageFileSize: 3760.53 KiB |
| BuildID:: MICSQTL_20230530124852 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MICSQTL. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘MICSQTL/DESCRIPTION’ ... OK
* preparing ‘MICSQTL’:
* 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 ‘MICSQTL_0.99.2.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('MICSQTL')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: MICSQTL
─ PackageVersion: 0.99.2
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3023/MICSQTL_20230530124852/MICSQTL
─ 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/3023/MICSQTL_20230530124852/MICSQTL.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MICSQTL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MICSQTL’ version ‘0.99.2’
* 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 ‘MICSQTL’ 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 ... [5s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
* checking loading without being on the library search path ... [5s/5s] 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 ... [18s/18s] 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 ... [4s/4s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] ERROR
Running examples in ‘MICSQTL-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TCA_deconv
> ### Title: Estimation of cellular expression in high-throughput data from
> ### heterogeneous tissues
> ### Aliases: TCA_deconv
>
> ### ** Examples
>
> data(se)
> se <- deconv(se, source = "protein", method = "cibersort")
Error in .check_ncores(cores) : 3 simultaneous processes spawned
Calls: deconv -> CIBERSORT -> CoreAlg -> mclapply -> .check_ncores
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [9s/9s]
[9s/9s] 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/6s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character ≥ (U+2265)
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: 2 ERRORs, 1 WARNING
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3023/MICSQTL_20230530124852/MICSQTL.Rcheck/00check.log’
for details.
===============================
BiocCheck('MICSQTL_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: MICSQTL
─ PackageVersion: 0.99.2
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp60iBpW/filea533aaee588/MICSQTL
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp60iBpW/filea533fbea30c
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3023/MICSQTL_20230530124852/MICSQTL.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 4.2.0 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...
* NOTE: Consider adding these automatically suggested biocViews:
Coverage
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...
* 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...
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
* 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 MICSQTL...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 7 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* 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; 26 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 75 lines
(3%) 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...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/
─ BiocCheck results ──
2 ERRORS | 1 WARNINGS | 8 NOTES
See the MICSQTL.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 MICSQTL_0.99.2.tar.gz'
>>>>>>>
* installing *source* package ‘MICSQTL’ ...
** 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 (MICSQTL)