merida1 Summary
[top]
| Package: terraTCGAdata |
| Version: 0.99.4 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data terraTCGAdata |
| BuildTime: 0 minutes 32.96 seconds |
| CheckCommand: BiocCheckGitClone('terraTCGAdata') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch terraTCGAdata_0.99.4.tar.gz && BiocCheck('terraTCGAdata_0.99.4.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 12.95 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh terraTCGAdata_0.99.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 22.93 seconds |
| PackageFileSize: 15.80 KiB |
| BuildID:: terraTCGAdata_20220420161314 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: terraTCGAdata. 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: 0. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘terraTCGAdata/DESCRIPTION’ ... OK
* preparing ‘terraTCGAdata’:
* 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
* building ‘terraTCGAdata_0.99.4.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('terraTCGAdata')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: terraTCGAdata
─ PackageVersion: 0.99.4
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2616/1e7129beffccda52814caf887b7d1fc9a3e40afe/terraTCGAdata
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output 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/2616/1e7129beffccda52814caf887b7d1fc9a3e40afe/terraTCGAdata.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 ‘terraTCGAdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘terraTCGAdata’ version ‘0.99.4’
* 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 ‘terraTCGAdata’ can be installed ... [21s/21s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... WARNING
Output(s) listed in 'build/vignette.rds' but not in package:
‘inst/doc/terraTCGAdata.html’
* 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 ... [22s/22s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'getAssayData.Rd':
\examples lines wider than 100 characters:
assayName = "protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data",
Rd file 'getTCGAdatalist.Rd':
\examples lines wider than 100 characters:
assayNames = c("protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data",
"snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg"),
These lines will be truncated in the PDF manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [7s/7s]
[7s/7s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Failed to locate ‘weave’ output file ‘terraTCGAdata.pdf’ or ‘terraTCGAdata.html’ for vignette with name ‘terraTCGAdata’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2616/1e7129beffccda52814caf887b7d1fc9a3e40afe/terraTCGAdata.Rcheck/00_pkg_src/terraTCGAdata/inst/doc’: ‘terraTCGAdata.R’ (2754 bytes), ‘terraTCGAdata.Rmd’ (4766 bytes)
Package vignette without corresponding single PDF/HTML:
‘terraTCGAdata.Rmd’
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2616/1e7129beffccda52814caf887b7d1fc9a3e40afe/terraTCGAdata.Rcheck/00check.log’
for details.
===============================
BiocCheck('terraTCGAdata_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: terraTCGAdata
─ PackageVersion: 0.99.4
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp9SI5I3/file5302679e16c/terraTCGAdata
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp9SI5I3/file530b275056
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2616/1e7129beffccda52814caf887b7d1fc9a3e40afe/terraTCGAdata.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...
* 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:
Normalization
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 terraTCGAdata...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 1
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
getClinicalTable.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 20 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 77 lines
(6%) 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...
Unable to connect to mailing list status code 502
* 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 terraTCGAdata.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 terraTCGAdata_0.99.4.tar.gz'
>>>>>>>
* installing *source* package ‘terraTCGAdata’ ...
** using staged installation
** R
** 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 (terraTCGAdata)
nebbiolo1 Summary
[top]
| Package: terraTCGAdata |
| Version: 0.99.4 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data terraTCGAdata |
| BuildTime: 0 minutes 22.92 seconds |
| CheckCommand: BiocCheckGitClone('terraTCGAdata') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings terraTCGAdata_0.99.4.tar.gz && BiocCheck('terraTCGAdata_0.99.4.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 8.28 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 15.82 KiB |
| BuildID:: terraTCGAdata_20220420161314 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: terraTCGAdata. 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: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘terraTCGAdata/DESCRIPTION’ ... OK
* preparing ‘terraTCGAdata’:
* 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
* building ‘terraTCGAdata_0.99.4.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('terraTCGAdata')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: terraTCGAdata
─ PackageVersion: 0.99.4
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2616/1e7129beffccda52814caf887b7d1fc9a3e40afe/terraTCGAdata
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output 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/2616/1e7129beffccda52814caf887b7d1fc9a3e40afe/terraTCGAdata.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 ‘terraTCGAdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘terraTCGAdata’ version ‘0.99.4’
* 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 ‘terraTCGAdata’ can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... WARNING
Output(s) listed in 'build/vignette.rds' but not in package:
‘inst/doc/terraTCGAdata.html’
* 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 ... [15s/15s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'getAssayData.Rd':
\examples lines wider than 100 characters:
assayName = "protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data",
Rd file 'getTCGAdatalist.Rd':
\examples lines wider than 100 characters:
assayNames = c("protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data",
"snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg"),
These lines will be truncated in the PDF manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [5s/5s]
[5s/5s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Failed to locate ‘weave’ output file ‘terraTCGAdata.pdf’ or ‘terraTCGAdata.html’ for vignette with name ‘terraTCGAdata’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2616/1e7129beffccda52814caf887b7d1fc9a3e40afe/terraTCGAdata.Rcheck/00_pkg_src/terraTCGAdata/inst/doc’: ‘terraTCGAdata.R’ (2754 bytes), ‘terraTCGAdata.Rmd’ (4766 bytes)
Package vignette without corresponding single PDF/HTML:
‘terraTCGAdata.Rmd’
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2616/1e7129beffccda52814caf887b7d1fc9a3e40afe/terraTCGAdata.Rcheck/00check.log’
for details.
===============================
BiocCheck('terraTCGAdata_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: terraTCGAdata
─ PackageVersion: 0.99.4
─ sourceDir: /tmp/RtmpflwBr5/file3f9a4c7f32c3fe/terraTCGAdata
─ installDir: /tmp/RtmpflwBr5/file3f9a4c2c1b893
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2616/1e7129beffccda52814caf887b7d1fc9a3e40afe/terraTCGAdata.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...
* 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:
Normalization
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 terraTCGAdata...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 1
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
getClinicalTable.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 20 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 77 lines
(6%) 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...
Unable to connect to mailing list status code 502
* 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 terraTCGAdata.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]