PICS 2.28.0
Renan Sauteraud
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/PICS |
| Branch: RELEASE_3_9 |
| Last Commit: 8cf1a4a |
| Last Changed Date: 2019-05-02 11:53:14 -0400 (Thu, 02 May 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PICS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PICS_2.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PICS.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PICS’ version ‘2.28.0’
* 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 ‘PICS’ can be installed ... WARNING
Found the following significant warnings:
pics.c:288:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
pics.c:296:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
pics.c:309:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
pics.c:317:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/PICS.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... 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 dependencies in R code ... NOTE
':::' calls which should be '::':
‘parallel:::detectCores’ ‘parallel:::makeCluster’
‘parallel:::parLapply’ ‘parallel:::stopCluster’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot,pics-segReads: warning in symbols((map[, 1] + map[, 2])/2,
rep(0.35, nMap), rectangle = cbind(map[, 2] - map[, 1], rep(0.6,
nMap)), inches = FALSE, bg = grey(0.6), fg = 0, add = TRUE, xlim =
c(m, M), ylim = c(0, 1)): partial argument match of 'rectangle' to
'rectangles'
plot,pics-segReads: warning in symbols(x@estimates$mu, rep(0.5, K), rec
= matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches =
FALSE, bg = grey(0.5 * pmin(se(x)/50, 1)), fg = 0, add = TRUE, xlim =
c(m, M), ylim = c(0, 1)): partial argument match of 'rec' to
'rectangles'
plot,pics-segReads: warning in symbols(x@estimates$mu, rep(0.5, K), rec
= matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches =
FALSE, fg = 0, bg = 1, add = TRUE, xlim = c(m, M), ylim = c(0, 1)):
partial argument match of 'rec' to 'rectangles'
bam2gr: no visible global function definition for ‘reshape’
Undefined global functions or variables:
reshape
Consider adding
importFrom("stats", "reshape")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'picsList,ANY,ANY,ANY'
generic '[' and siglist 'segReadsList,ANY,ANY,ANY'
generic '[' and siglist 'segReadsListPE,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/PICS.Rcheck/00check.log’
for details.