nebbiolo1 Summary
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| Package: pareg |
| Version: 0.99.3 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data pareg |
| BuildTime: 0 minutes 50.30 seconds |
| CheckCommand: BiocCheckGitClone('pareg') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings pareg_0.99.3.tar.gz && BiocCheck('pareg_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 13 minutes 25.00 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 637.61 KiB |
| BuildID:: pareg_20220225142353 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: pareg. 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. WARNING: check time exceeded 10 min. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘pareg/DESCRIPTION’ ... OK
* preparing ‘pareg’:
* 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 ‘pareg_0.99.3.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('pareg')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2537/7edd164c6534863f1222f8598dd0d767fa4de2d8/pareg.Rcheck’
* using R Under development (unstable) (2022-02-17 r81757)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pareg/DESCRIPTION’ ... OK
* this is package ‘pareg’ version ‘0.99.3’
* 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 ‘pareg’ can be installed ... [7s/8s] 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 ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [71s/66s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
as.data.frame.pareg 20.648 4.262 19.848
pareg 17.374 0.053 17.426
plot_pareg_with_args 17.228 0.063 17.289
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [11m/11m]
[11m/11m] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘circlize’
* 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: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2537/7edd164c6534863f1222f8598dd0d767fa4de2d8/pareg.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('pareg_0.99.3.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2537/7edd164c6534863f1222f8598dd0d767fa4de2d8/pareg_0.99.3.tar.gz" "/tmp/Rtmp1SQQnh/file3c679c746d71be/lib" 2>/dev/null' had status 1
* 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 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...
* 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 vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/pareg.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of pareg...
* Checking coding practice...
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/main.R (line 79, column 12)
R/netreg.R (line 209, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 8 functions > 50 lines.
The longest 5 functions are:
pareg() (R/main.R, line 42): 104 lines
plot_pareg_with_args() (R/plotting.R, line 39): 90 lines
_anonymous_.998() (R/netreg.R, line 998): 89 lines
.cv.edgenet() (R/netreg.R, line 1092): 88 lines
.edgenet() (R/netreg.R, line 1422): 77 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; 8 lines (0%) are > 80 characters
long.
First 6 lines:
vignettes/pareg.Rmd:17 It estimates pathway enrichment scores by regres...
vignettes/pareg.Rmd:18 These scores are computed using a regularized ge...
vignettes/pareg.Rmd:19 The network regularization term is based on a pa...
vignettes/pareg.Rmd:32 We start our analysis by loading the `pareg` pac...
vignettes/pareg.Rmd:48 For the sake of this introductory example, we ge...
vignettes/pareg.Rmd:80 Before starting the actual enrichment estimation...
* NOTE: Consider multiples of 4 spaces for line indents, 893
lines(29%) are not.
First 6 lines:
R/main.R:43 df_genes,
R/main.R:44 df_terms,
R/main.R:45 lasso_param = NA_real_,
R/main.R:46 network_param = NA_real_,
R/main.R:47 term_network = NULL,
R/main.R:48 cv = FALSE,
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.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 6
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
nebbiolo1 BUILD BIN output
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merida1 Summary
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| Package: pareg |
| Version: 0.99.3 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pareg |
| BuildTime: 3 minutes 4.31 seconds |
| CheckCommand: BiocCheckGitClone('pareg') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pareg_0.99.3.tar.gz && BiocCheck('pareg_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 14 minutes 59.96 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh pareg_0.99.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 29.17 seconds |
| PackageFileSize: 631.95 KiB |
| BuildID:: pareg_20220225142353 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: pareg. 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: -9. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘pareg/DESCRIPTION’ ... OK
* preparing ‘pareg’:
* 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 ‘pareg_0.99.3.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('pareg')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2537/7edd164c6534863f1222f8598dd0d767fa4de2d8/pareg.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pareg/DESCRIPTION’ ... OK
* this is package ‘pareg’ version ‘0.99.3’
* 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 ‘pareg’ can be installed ... [23s/24s] 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 ... NOTE
package 'methods' is used but not declared
* 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 ... [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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [227s/243s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
as.data.frame.pareg 71.610 1.327 76.428
pareg 60.907 0.179 66.453
plot_pareg_with_args 60.159 0.153 67.267
cvedgenet-methods 14.186 0.086 14.474
edgenet-methods 6.488 0.026 6.539
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 14 mins
===============================
BiocCheck('pareg_0.99.3.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2537/7edd164c6534863f1222f8598dd0d767fa4de2d8/pareg_0.99.3.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp8gT50r/file88287a38d39c/lib" 2>/dev/null' had status 1
* 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 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...
* 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 vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/pareg.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of pareg...
* Checking coding practice...
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/main.R (line 79, column 12)
R/netreg.R (line 209, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 8 functions > 50 lines.
The longest 5 functions are:
pareg() (R/main.R, line 42): 104 lines
plot_pareg_with_args() (R/plotting.R, line 39): 90 lines
_anonymous_.998() (R/netreg.R, line 998): 89 lines
.cv.edgenet() (R/netreg.R, line 1092): 88 lines
.edgenet() (R/netreg.R, line 1422): 77 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; 8 lines (0%) are > 80 characters
long.
First 6 lines:
vignettes/pareg.Rmd:17 It estimates pathway enrichment scores by regres...
vignettes/pareg.Rmd:18 These scores are computed using a regularized ge...
vignettes/pareg.Rmd:19 The network regularization term is based on a pa...
vignettes/pareg.Rmd:32 We start our analysis by loading the `pareg` pac...
vignettes/pareg.Rmd:48 For the sake of this introductory example, we ge...
vignettes/pareg.Rmd:80 Before starting the actual enrichment estimation...
* NOTE: Consider multiples of 4 spaces for line indents, 893
lines(29%) are not.
First 6 lines:
R/main.R:43 df_genes,
R/main.R:44 df_terms,
R/main.R:45 lasso_param = NA_real_,
R/main.R:46 network_param = NA_real_,
R/main.R:47 term_network = NULL,
R/main.R:48 cv = FALSE,
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.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 6
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir pareg_0.99.3.tar.gz'
>>>>>>>
* installing *source* package ‘pareg’ ...
** 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 (pareg)