nebbiolo1 Summary
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Package: crisprScore |
Version: 0.99.13 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data crisprScore |
BuildTime: 0 minutes 28.46 seconds |
CheckCommand: BiocCheckGitClone('crisprScore') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings crisprScore_0.99.13.tar.gz && BiocCheck('crisprScore_0.99.13.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 19.98 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 2556.18 KiB |
BuildID:: crisprScore_20211218015016 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: crisprScore. 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
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===============================
R CMD BUILD
===============================
* checking for file ‘crisprScore/DESCRIPTION’ ... OK
* preparing ‘crisprScore’:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘crisprScore/data/scoringMethodsInfo.rda’
‘crisprScore/inst/cfd_cas9/cfd.mm.scores.cas9.rda’
‘crisprScore/inst/cfd_cas9/cfd.mm.weights.cas9.rda’
‘crisprScore/inst/cfd_cas9/cfd.pam.scores.cas9.rda’
‘crisprScore/inst/cfd_cas9/cfd.pam.weights.cas9.rda’
‘crisprScore/inst/mit/mit.weights.rda’
* building ‘crisprScore_0.99.13.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('crisprScore')
===============================
This is BiocCheckGitClone version 1.31.15. 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/2155/652c549a99334b84fbfdb1a335b25f6508cce0bf/crisprScore.Rcheck’
* using R Under development (unstable) (2021-11-10 r81171)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprScore/DESCRIPTION’ ... OK
* this is package ‘crisprScore’ version ‘0.99.13’
* 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 ‘crisprScore’ can be installed ... [18s/18s] NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2155/652c549a99334b84fbfdb1a335b25f6508cce0bf/crisprScore.Rcheck/00install.out’ for details.
* 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 ... [24s/25s] 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in shell scripts ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [8s/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 ... OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2155/652c549a99334b84fbfdb1a335b25f6508cce0bf/crisprScore.Rcheck/00check.log’
for details.
===============================
BiocCheck('crisprScore_0.99.13.tar.gz')
===============================
This is BiocCheck version 1.31.15. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
snapshotDate(): 2021-11-24
* 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...
* NOTE: Update R version dependency from 3.5.0 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of crisprScore...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths * NOTE: Recommended function length <= 50 lines.
There are 1 functions > 50 lines.
The longest 5 functions are:
.ruleset1_engine() (R/getRuleSet1Scores.R, line 76): 59 lines
getCFDScores() (R/getCFDScores.R, line 36): 47 lines
getMITScores() (R/getMITScores.R, line 36): 43 lines
getDeepHFScores() (R/getDeepHFScores.R, line 61): 41 lines
.lindel_python() (R/getLindelScores.R, line 61): 36 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; 2 lines (0%) are > 80 characters
long.
First 2 lines:
R/getRuleSet1Scores.R:24 #' for CRISPR-Cas9–mediated gene inactivat...
man/getRuleSet1Scores.Rd:43 for CRISPR-Cas9–mediated gene inactivat...
* NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain
tabs.
First 3 lines:
R/getDeepHFScores.R:65 if (.Platform$OS.type=="windows"){
R/getDeepHFScores.R:66 stop("DeepHF is not available for Windows at t...
R/getDeepHFScores.R:67 }
* NOTE: Consider multiples of 4 spaces for line indents, 268
lines(14%) are not.
First 6 lines:
R/basilisk.R:2 "biopython==1.74",
R/basilisk.R:3 "certifi==2019.11.28",
R/basilisk.R:4 "cycler==0.10.0",
R/basilisk.R:5 "futures==3.3.0",
R/basilisk.R:6 "kiwisolver==1.1.0",
R/basilisk.R:7 "matplotlib==2.2.3",
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: 5
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: crisprScore |
Version: 0.99.13 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data crisprScore |
BuildTime: 1 minutes 3.43 seconds |
CheckCommand: BiocCheckGitClone('crisprScore') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch crisprScore_0.99.13.tar.gz && BiocCheck('crisprScore_0.99.13.tar.gz', `new-package`=TRUE) |
CheckTime: 6 minutes 11.01 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh crisprScore_0.99.13.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 30.05 seconds |
PackageFileSize: 2556.17 KiB |
BuildID:: crisprScore_20211218015016 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: crisprScore. 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 ‘crisprScore/DESCRIPTION’ ... OK
* preparing ‘crisprScore’:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘crisprScore/data/scoringMethodsInfo.rda’
‘crisprScore/inst/cfd_cas9/cfd.mm.scores.cas9.rda’
‘crisprScore/inst/cfd_cas9/cfd.mm.weights.cas9.rda’
‘crisprScore/inst/cfd_cas9/cfd.pam.scores.cas9.rda’
‘crisprScore/inst/cfd_cas9/cfd.pam.weights.cas9.rda’
‘crisprScore/inst/mit/mit.weights.rda’
* building ‘crisprScore_0.99.13.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('crisprScore')
===============================
This is BiocCheckGitClone version 1.31.15. 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/2155/652c549a99334b84fbfdb1a335b25f6508cce0bf/crisprScore.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprScore/DESCRIPTION’ ... OK
* this is package ‘crisprScore’ version ‘0.99.13’
* 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 ‘crisprScore’ can be installed ... [37s/39s] NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/2155/652c549a99334b84fbfdb1a335b25f6508cce0bf/crisprScore.Rcheck/00install.out’ for details.
* 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 ... [50s/53s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in shell scripts ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/16s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [13s/13s]
[13s/14s] 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 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2155/652c549a99334b84fbfdb1a335b25f6508cce0bf/crisprScore.Rcheck/00check.log’
for details.
===============================
BiocCheck('crisprScore_0.99.13.tar.gz')
===============================
This is BiocCheck version 1.31.15. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
snapshotDate(): 2021-11-24
* 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...
* NOTE: Update R version dependency from 3.5.0 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of crisprScore...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths * NOTE: Recommended function length <= 50 lines.
There are 1 functions > 50 lines.
The longest 5 functions are:
.ruleset1_engine() (R/getRuleSet1Scores.R, line 76): 59 lines
getCFDScores() (R/getCFDScores.R, line 36): 47 lines
getMITScores() (R/getMITScores.R, line 36): 43 lines
getDeepHFScores() (R/getDeepHFScores.R, line 61): 41 lines
.lindel_python() (R/getLindelScores.R, line 61): 36 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; 2 lines (0%) are > 80 characters
long.
First 2 lines:
R/getRuleSet1Scores.R:24 #' for CRISPR-Cas9–mediated gene inactivat...
man/getRuleSet1Scores.Rd:43 for CRISPR-Cas9–mediated gene inactivat...
* NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain
tabs.
First 3 lines:
R/getDeepHFScores.R:65 if (.Platform$OS.type=="windows"){
R/getDeepHFScores.R:66 stop("DeepHF is not available for Windows at t...
R/getDeepHFScores.R:67 }
* NOTE: Consider multiples of 4 spaces for line indents, 268
lines(14%) are not.
First 6 lines:
R/basilisk.R:2 "biopython==1.74",
R/basilisk.R:3 "certifi==2019.11.28",
R/basilisk.R:4 "cycler==0.10.0",
R/basilisk.R:5 "futures==3.3.0",
R/basilisk.R:6 "kiwisolver==1.1.0",
R/basilisk.R:7 "matplotlib==2.2.3",
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: 5
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 crisprScore_0.99.13.tar.gz'
>>>>>>>
* installing *source* package ‘crisprScore’ ...
** using non-staged installation via StagedInstall field
** R
** data
** inst
** byte-compile and prepare package for lazy loading
snapshotDate(): 2021-11-24
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
snapshotDate(): 2021-11-24
* DONE (crisprScore)