BioQC 1.2.0
Jitao David Zhang
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/BioQC | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BioQC_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/BioQC.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioQC’ version ‘1.2.0’
* 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 ‘BioQC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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 ... NOTE
rankSumTestWithCorrelation: no visible global function definition for
‘pt’
wmw.test: no visible global function definition for ‘wilcox.test’
wmwTest: no visible global function definition for ‘is’
Undefined global functions or variables:
is pt wilcox.test
Consider adding
importFrom("methods", "is")
importFrom("stats", "pt", "wilcox.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/BioQC.Rcheck/00check.log’
for details.
* installing *source* package ‘BioQC’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG `/home/biocbuild/bbs-3.4-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include -fpic -g -O2 -Wall -c bioqc.c -o bioqc.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG `/home/biocbuild/bbs-3.4-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include -fpic -g -O2 -Wall -c gini.c -o gini.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG `/home/biocbuild/bbs-3.4-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include -fpic -g -O2 -Wall -c read_gmt.cpp -o read_gmt.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG `/home/biocbuild/bbs-3.4-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include -fpic -g -O2 -Wall -c stat_rank.c -o stat_rank.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG `/home/biocbuild/bbs-3.4-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include -fpic -g -O2 -Wall -c wmw_test_R.c -o wmw_test_R.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o BioQC.so bioqc.o gini.o read_gmt.o stat_rank.o wmw_test_R.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/BioQC.Rcheck/BioQC/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BioQC)