nebbiolo1 Summary
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| Package: PSMatch |
| Version: 0.99.1 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PSMatch |
| BuildTime: 1 minutes 2.04 seconds |
| CheckCommand: BiocCheckGitClone('PSMatch') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings PSMatch_0.99.1.tar.gz && BiocCheck('PSMatch_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 9.72 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 1326.45 KiB |
| BuildID:: PSMatch_20220308151258 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: PSMatch. 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
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===============================
R CMD BUILD
===============================
* checking for file ‘PSMatch/DESCRIPTION’ ... OK
* preparing ‘PSMatch’:
* 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 ‘PSMatch_0.99.1.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('PSMatch')
===============================
This is BiocCheckGitClone version 1.31.36. 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...
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/2529/78e6bc893ecf15aa77a6d8475e4680ad84bf18a5/PSMatch.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 ‘PSMatch/DESCRIPTION’ ... OK
* this is package ‘PSMatch’ 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 serialization versions ... OK
* checking whether package ‘PSMatch’ can be installed ... [16s/16s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [17s/17s] 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 ... [36s/38s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PSM 21.424 0.348 23.433
* checking for unstated dependencies in ‘tests’ ... WARNING
'::' or ':::' import not declared from: ‘IRanges’
* checking tests ...
Running ‘testthat.R’ [20s/20s]
[20s/20s] 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 ... OK
* DONE
Status: 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2529/78e6bc893ecf15aa77a6d8475e4680ad84bf18a5/PSMatch.Rcheck/00check.log’
for details.
===============================
BiocCheck('PSMatch_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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/2529/78e6bc893ecf15aa77a6d8475e4680ad84bf18a5/PSMatch_0.99.1.tar.gz" "/tmp/Rtmprh8hog/file13907f6fa347f9/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...
* 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:
SequenceMatching
See http://bioconductor.org/developers/how-to/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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of PSMatch...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/PSM-reduce.R (line 23, column 15)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
fragments-calculate.R (line 188, column 36)
PSM-class.R (line 235, column 43)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/PSM-class.R (line 203, column 5)
cat() in R/PSM-class.R (line 204, column 5)
cat() in R/PSM-class.R (line 207, column 5)
cat() in R/PSM-class.R (line 208, column 5)
cat() in R/PSM-class.R (line 212, column 5)
cat() in R/PSM-class.R (line 213, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 3 functions > 50 lines.
The longest 5 functions are:
.calculateFragments() (R/fragments-calculate.R, line 126): 98
lines
plotAdjacencyMatrix() (R/adjacencyMatrix-plot.R, line 36): 67
lines
PSM() (R/PSM-class.R, line 282): 61 lines
.neutralLoss() (R/fragments-calculate.R, line 228): 48 lines
getAminoAcids() (R/fragments-utils.R, line 17): 47 lines
* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following man
pages: man/ConnectedComponents.Rd
* 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; 81 lines (2%) are > 80 characters
long.
First 6 lines:
R/adjacencyMatrix-accessors.R:10 stop("Please define ...
R/adjacencyMatrix-create.R:136 ##' peptide = paste0...
R/adjacencyMatrix-create.R:137 ##' protein = paste0...
R/adjacencyMatrix-create.R:185 ##' "Pro...
R/adjacencyMatrix-plot.R:1 ##' @importFrom igraph layout_nicely graph_f...
R/adjacencyMatrix-plot.R:48 stop("Please provide colours fo...
* NOTE: Consider multiples of 4 spaces for line indents, 326
lines(8%) are not.
First 6 lines:
R/adjacencyMatrix-accessors.R:7 function(object) {
R/adjacencyMatrix-accessors.R:8 if (is.na(psmVariables(ob...
R/adjacencyMatrix-accessors.R:9 is.na(psmVariables(ob...
R/adjacencyMatrix-accessors.R:10 stop("Please define ...
R/adjacencyMatrix-accessors.R:11 if (!psmVariables(object...
R/adjacencyMatrix-accessors.R:12 !psmVariables(object...
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.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 1
WARNING count: 1
NOTE count: 7
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
BiocCheck FAILED.
nebbiolo1 BUILD BIN output
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merida1 Summary
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| Package: PSMatch |
| Version: 0.99.1 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data PSMatch |
| BuildTime: 1 minutes 19.43 seconds |
| CheckCommand: BiocCheckGitClone('PSMatch') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PSMatch_0.99.1.tar.gz && BiocCheck('PSMatch_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 22.59 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh PSMatch_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 23.13 seconds |
| PackageFileSize: 1312.37 KiB |
| BuildID:: PSMatch_20220308151258 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: PSMatch. 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 ‘PSMatch/DESCRIPTION’ ... OK
* preparing ‘PSMatch’:
* 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 ‘PSMatch_0.99.1.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('PSMatch')
===============================
This is BiocCheckGitClone version 1.31.36. 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...
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/2529/78e6bc893ecf15aa77a6d8475e4680ad84bf18a5/PSMatch.Rcheck’
* using R Under development (unstable) (2022-03-02 r81842)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PSMatch/DESCRIPTION’ ... OK
* this is package ‘PSMatch’ 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 serialization versions ... OK
* checking whether package ‘PSMatch’ can be installed ... [23s/23s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [23s/23s] 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 ... [49s/56s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PSM 30.427 0.326 37.32
* checking for unstated dependencies in ‘tests’ ... WARNING
'::' or ':::' import not declared from: ‘IRanges’
* checking tests ...
Running ‘testthat.R’ [27s/27s]
[27s/27s] 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 ... OK
* DONE
Status: 1 WARNING
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2529/78e6bc893ecf15aa77a6d8475e4680ad84bf18a5/PSMatch.Rcheck/00check.log’
for details.
===============================
BiocCheck('PSMatch_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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/2529/78e6bc893ecf15aa77a6d8475e4680ad84bf18a5/PSMatch_0.99.1.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpmnighl/fileab85602b3589/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...
* 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:
SequenceMatching
See http://bioconductor.org/developers/how-to/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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of PSMatch...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/PSM-reduce.R (line 23, column 15)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
fragments-calculate.R (line 188, column 36)
PSM-class.R (line 235, column 43)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/PSM-class.R (line 203, column 5)
cat() in R/PSM-class.R (line 204, column 5)
cat() in R/PSM-class.R (line 207, column 5)
cat() in R/PSM-class.R (line 208, column 5)
cat() in R/PSM-class.R (line 212, column 5)
cat() in R/PSM-class.R (line 213, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 3 functions > 50 lines.
The longest 5 functions are:
.calculateFragments() (R/fragments-calculate.R, line 126): 98
lines
plotAdjacencyMatrix() (R/adjacencyMatrix-plot.R, line 36): 67
lines
PSM() (R/PSM-class.R, line 282): 61 lines
.neutralLoss() (R/fragments-calculate.R, line 228): 48 lines
getAminoAcids() (R/fragments-utils.R, line 17): 47 lines
* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following man
pages: man/ConnectedComponents.Rd
* 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; 81 lines (2%) are > 80 characters
long.
First 6 lines:
R/adjacencyMatrix-accessors.R:10 stop("Please define ...
R/adjacencyMatrix-create.R:136 ##' peptide = paste0...
R/adjacencyMatrix-create.R:137 ##' protein = paste0...
R/adjacencyMatrix-create.R:185 ##' "Pro...
R/adjacencyMatrix-plot.R:1 ##' @importFrom igraph layout_nicely graph_f...
R/adjacencyMatrix-plot.R:48 stop("Please provide colours fo...
* NOTE: Consider multiples of 4 spaces for line indents, 326
lines(8%) are not.
First 6 lines:
R/adjacencyMatrix-accessors.R:7 function(object) {
R/adjacencyMatrix-accessors.R:8 if (is.na(psmVariables(ob...
R/adjacencyMatrix-accessors.R:9 is.na(psmVariables(ob...
R/adjacencyMatrix-accessors.R:10 stop("Please define ...
R/adjacencyMatrix-accessors.R:11 if (!psmVariables(object...
R/adjacencyMatrix-accessors.R:12 !psmVariables(object...
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.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 1
WARNING count: 1
NOTE count: 7
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
BiocCheck FAILED.
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir PSMatch_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘PSMatch’ ...
** 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 (PSMatch)