===============================
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_0.99.9.tar.gz’
===============================
BiocCheckGitClone('crisprScore')
===============================
This is BiocCheckGitClone version 1.29.14. 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/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2155/crisprScore_20211005122555/crisprScore.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘0.99.9’
* 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 ... [16s/17s] NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2155/crisprScore_20211005122555/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 ... [22s/24s] 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 ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [6s/7s]
[6s/7s] 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/crisprScore_20211005122555/crisprScore.Rcheck/00check.log’
for details.
===============================
BiocCheck('crisprScore_0.99.9.tar.gz')
===============================
This is BiocCheck version 1.29.14. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
snapshotDate(): 2021-10-05
* 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 4.1.0.
* 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 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...................
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
getAzimuthScores.Rd, getDeepCpf1Scores.Rd, getDeepHFScores.Rd,
getEnPAMGBScores.Rd, getLindelScores.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
45% of man pages use one of these cases.
Found in the following files:
getAzimuthScores.Rd
getDeepCpf1Scores.Rd
getDeepHFScores.Rd
getEnPAMGBScores.Rd
getLindelScores.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
getAzimuthScores.Rd
getDeepCpf1Scores.Rd
getDeepHFScores.Rd
getEnPAMGBScores.Rd
getLindelScores.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 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, 257
lines(15%) 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: 1
WARNING count: 0
NOTE count: 5
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.