===============================
R CMD BUILD
===============================
* checking for file ‘SARC/DESCRIPTION’ ... OK
* preparing ‘SARC’:
* 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
* building ‘SARC_0.99.232.tar.gz’
===============================
BiocCheckGitClone('SARC')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: SARC
─ PackageVersion: 0.99.232
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3071/5ca782f360609a9eceee67c3a0477001848b4fb3/SARC
─ 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...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3071/5ca782f360609a9eceee67c3a0477001848b4fb3/SARC.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 ‘SARC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SARC’ version ‘0.99.232’
* 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 ‘SARC’ 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [27s/27s] NOTE
addExonsGenes: no visible global function definition for ‘metadata’
addExonsGenes: no visible global function definition for ‘metadata<-’
anovaOnCNV: no visible global function definition for ‘metadata’
anovaOnCNV: no visible global function definition for ‘metadata<-’
cnvConfidence: no visible global function definition for ‘metadata’
cnvConfidence: no visible global function definition for ‘metadata<-’
pasteExonsGenes: no visible global function definition for ‘metadata’
pasteExonsGenes: no visible global function definition for ‘metadata<-’
phDunnetonCNV: no visible global function definition for ‘metadata’
phDunnetonCNV: no visible global function definition for ‘metadata<-’
plotCovPrep: no visible global function definition for ‘metadata’
plotCovPrep: no visible global function definition for ‘metadata<-’
prepAnova: no visible global function definition for ‘metadata’
prepAnova: no visible global function definition for ‘metadata<-’
regionGrangeMake: no visible global function definition for ‘metadata’
regionGrangeMake: no visible global function definition for
‘metadata<-’
regionMean: no visible global function definition for ‘metadata’
regionMean: no visible global function definition for ‘metadata<-’
regionQuantiles: no visible global function definition for ‘metadata’
regionQuantiles: no visible global function definition for ‘metadata<-’
regionSet: no visible global function definition for ‘sortSeqlevels’
regionSet: no visible global function definition for ‘metadata’
regionSet: no visible global function definition for ‘metadata<-’
regionSplit: no visible global function definition for ‘metadata’
regionSplit: no visible global function definition for ‘metadata<-’
setQDplot: no visible global function definition for ‘metadata’
setQDplot: no visible global function definition for ‘metadata<-’
setupCNVplot: no visible global function definition for ‘metadata’
setupCNVplot: no visible global function definition for ‘metadata<-’
Undefined global functions or variables:
metadata metadata<- sortSeqlevels
* 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 ... WARNING
Codoc mismatches from documentation object 'pasteExonsGenes':
pasteExonsGenes
Code: function(RE, setup, cnv, nameofnewdf = "CNVexonsgenes")
Docs: function(RE, setup, cnv, nameofnewdf = "cnvExonsGenes")
Mismatches in argument default values:
Name: 'nameofnewdf' Code: "CNVexonsgenes" Docs: "cnvExonsGenes"
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [107s/107s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCNV 33.854 0.496 34.350
addExonsGenes 19.414 0.481 19.898
pasteExonsGenes 13.896 0.276 14.174
setupCNVplot 13.467 0.228 13.697
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [30s/30s]
[30s/30s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
Loading required package: GenomeInfoDb
> test_check(package = "SARC")
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 24 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_plotCNV.R:7:1'): (code run outside of `test_that()`) ───────────
Error in `gzfile(file, "rb")`: cannot open the connection
Backtrace:
▆
1. └─base::readRDS("tests/testthat/test1.rds") at test_plotCNV.R:7:0
2. └─base::gzfile(file, "rb")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 24 ]
Error: Test failures
Execution halted
* 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: 1 ERROR, 1 WARNING, 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3071/5ca782f360609a9eceee67c3a0477001848b4fb3/SARC.Rcheck/00check.log’
for details.
===============================
BiocCheck('SARC_0.99.232.tar.gz')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: SARC
─ PackageVersion: 0.99.232
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmpxoa9N0/file1676148f6c64c/SARC
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmpxoa9N0/file16761265edc82
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3071/5ca782f360609a9eceee67c3a0477001848b4fb3/SARC.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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:
Coverage
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...
* Checking License: for restrictive use...
* 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 SARC...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/addExonsGenes.Rd
Found @ in man/pasteExonsGenes.Rd
Found @ in man/plotCNV.Rd
Found @ in man/setupCNVplot.Rd
Found @ in vignettes/SARC_guide.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 11 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* 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; 322 lines (11%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 591 lines
(20%) 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 | 10 NOTES
See the SARC.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir SARC_0.99.232.tar.gz'
>>>>>>>
* installing *source* package ‘SARC’ ...
** using staged installation
** R
** data
** 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 (SARC)
===============================
R CMD BUILD
===============================
* checking for file ‘SARC/DESCRIPTION’ ... OK
* preparing ‘SARC’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘SARC’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘RaggedExperiment’ in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘Matrix’
Execution halted
ERROR: lazy loading failed for package ‘SARC’
* removing ‘/tmp/RtmpQm15QP/Rinst5a444550a9130/SARC’
-----------------------------------
ERROR: package installation failed