nebbiolo2 Summary
[top]
| Package: Moonlight2R |
| Version: 0.99.8 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Moonlight2R |
| BuildTime: 2 minutes 18.11 seconds |
| CheckCommand: BiocCheckGitClone('Moonlight2R') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2993/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2993/ea2143af6dc037ee3c87b1f698f1a691d7b0afb4/Moonlight2R.install-out.txt Moonlight2R_0.99.8.tar.gz && BiocCheck('Moonlight2R_0.99.8.tar.gz', `new-package`=TRUE) |
| CheckTime: 8 minutes 25.66 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4814.89 KiB |
| BuildID:: Moonlight2R_20230824115211 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: Moonlight2R. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* preparing ‘Moonlight2R’:
* 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 ‘Moonlight2R_0.99.8.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('Moonlight2R')
===============================
─ BiocCheckVersion: 1.37.10
─ BiocVersion: 3.18
─ Package: Moonlight2R
─ PackageVersion: 0.99.8
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2993/ea2143af6dc037ee3c87b1f698f1a691d7b0afb4/Moonlight2R
─ 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...
* Checking that provided CITATION file is correctly formatted...
* NOTE: CITATION file might be not correctly formatted
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2993/ea2143af6dc037ee3c87b1f698f1a691d7b0afb4/Moonlight2R.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ version ‘0.99.8’
* 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 ‘Moonlight2R’ 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 ... [18s/19s] OK
* checking whether the package can be loaded with stated dependencies ... [17s/18s] OK
* checking whether the package can be unloaded cleanly ... [17s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [17s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [17s/18s] OK
* checking loading without being on the library search path ... [17s/18s] 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/57s] NOTE
Found the following calls to data() loading into the global environment:
File ‘Moonlight2R/R/DMA.R’:
data("LOC_transcription")
data("LOC_translation")
data("LOC_protein")
File ‘Moonlight2R/R/FEA.R’:
data("DiseaseList")
data("EAGenes")
File ‘Moonlight2R/R/PRA.R’:
data("tabGrowBlock")
data("knownDriverGenes")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'GLS.Rd':
\examples lines wider than 100 characters:
query_string = "AND cancer AND driver AND '1980/01/01'[Date - Publication] : '2023/01/01'[Date - Publication]")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [83s/76s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GRN 8.461 0.000 0.155
LiftMAF 5.731 0.614 6.969
plotFEA 5.596 0.232 5.828
plotMoonlight 5.092 0.224 5.316
GLS 4.631 0.049 5.798
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [55s/48s]
[55s/48s] 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] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2993/ea2143af6dc037ee3c87b1f698f1a691d7b0afb4/Moonlight2R.Rcheck/00check.log’
for details.
===============================
BiocCheck('Moonlight2R_0.99.8.tar.gz')
===============================
─ BiocCheckVersion: 1.37.10
─ BiocVersion: 3.18
─ Package: Moonlight2R
─ PackageVersion: 0.99.8
─ sourceDir: /tmp/RtmppyeT3g/file10410c2c5fec6/Moonlight2R
─ installDir: /tmp/RtmppyeT3g/file10410c459594ae
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2993/ea2143af6dc037ee3c87b1f698f1a691d7b0afb4/Moonlight2R.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 4.2 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:
DriverMutation, SomaticMutation
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...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking for recommeded fields in DESCRIPTION...
* 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 Moonlight2R...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* 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 13 functions greater than 50 lines.
* Checking man page documentation...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 6% of man pages use at least one of these tags.
* 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; 433 lines (8%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 60 lines (1%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 860 lines
(16%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 13 NOTES
See the Moonlight2R.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]
lconway Summary
[top]
| Package: Moonlight2R |
| Version: 0.99.8 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Moonlight2R |
| BuildTime: 1 minutes 47.12 seconds |
| CheckCommand: BiocCheckGitClone('Moonlight2R') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2993/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2993/ea2143af6dc037ee3c87b1f698f1a691d7b0afb4/Moonlight2R.install-out.txt Moonlight2R_0.99.8.tar.gz && BiocCheck('Moonlight2R_0.99.8.tar.gz', `new-package`=TRUE) |
| CheckTime: 6 minutes 49.78 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh Moonlight2R_0.99.8.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 48.94 seconds |
| PackageFileSize: 4814.66 KiB |
| BuildID:: Moonlight2R_20230824115211 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: Moonlight2R. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* preparing ‘Moonlight2R’:
* 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 ‘Moonlight2R_0.99.8.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('Moonlight2R')
===============================
─ BiocCheckVersion: 1.37.10
─ BiocVersion: 3.18
─ Package: Moonlight2R
─ PackageVersion: 0.99.8
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2993/ea2143af6dc037ee3c87b1f698f1a691d7b0afb4/Moonlight2R
─ 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...
* Checking that provided CITATION file is correctly formatted...
* NOTE: CITATION file might be not correctly formatted
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2993/ea2143af6dc037ee3c87b1f698f1a691d7b0afb4/Moonlight2R.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ version ‘0.99.8’
* 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 ‘Moonlight2R’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [13s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/14s] OK
* checking whether the package can be unloaded cleanly ... [13s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/14s] OK
* checking loading without being on the library search path ... [13s/14s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [41s/44s] NOTE
Found the following calls to data() loading into the global environment:
File ‘Moonlight2R/R/DMA.R’:
data("LOC_transcription")
data("LOC_translation")
data("LOC_protein")
File ‘Moonlight2R/R/FEA.R’:
data("DiseaseList")
data("EAGenes")
File ‘Moonlight2R/R/PRA.R’:
data("tabGrowBlock")
data("knownDriverGenes")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'GLS.Rd':
\examples lines wider than 100 characters:
query_string = "AND cancer AND driver AND '1980/01/01'[Date - Publication] : '2023/01/01'[Date - Publication]")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [54s/65s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
LiftMAF 3.937 0.458 5.121
GLS 3.063 1.051 12.621
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [33s/36s]
[33s/36s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2993/ea2143af6dc037ee3c87b1f698f1a691d7b0afb4/Moonlight2R.Rcheck/00check.log’
for details.
===============================
BiocCheck('Moonlight2R_0.99.8.tar.gz')
===============================
─ BiocCheckVersion: 1.37.10
─ BiocVersion: 3.18
─ Package: Moonlight2R
─ PackageVersion: 0.99.8
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpkrKDji/file119aa303e8ab2/Moonlight2R
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpkrKDji/file119aa2d7175af
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2993/ea2143af6dc037ee3c87b1f698f1a691d7b0afb4/Moonlight2R.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 4.2 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:
DriverMutation, SomaticMutation
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...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking for recommeded fields in DESCRIPTION...
* 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 Moonlight2R...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* 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 13 functions greater than 50 lines.
* Checking man page documentation...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 6% of man pages use at least one of these tags.
* 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; 433 lines (8%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 60 lines (1%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 860 lines
(16%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 13 NOTES
See the Moonlight2R.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 Moonlight2R_0.99.8.tar.gz'
>>>>>>>
* installing *source* package ‘Moonlight2R’ ...
** 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 (Moonlight2R)