genoCN 1.21.0
Wei Sun
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genoCN | | Last Changed Rev: 102594 / Revision: 107696 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings genoCN_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/genoCN.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoCN’ version ‘1.21.0’
* 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 ‘genoCN’ can be installed ... [2s/2s] 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
genoCNA: no visible binding for global variable ‘init.Para.CNA’
genoCNV: no visible binding for global variable ‘init.Para.CNV’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
genoCNA 13.52 0.056 13.616
* 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-3.2-bioc/meat/genoCN.Rcheck/00check.log’
for details.
* installing *source* package ‘genoCN’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tnorm_mle.c -o tnorm_mle.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utility.c -o utility.o
utility.c: In function ‘readfile’:
utility.c:155:19: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf(file,"%s",temp);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c xCNV.c -o xCNV.o
xCNV.c: In function ‘emiss’:
xCNV.c:317:25: warning: unused variable ‘k’ [-Wunused-variable]
int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
^
xCNV.c:317:16: warning: unused variable ‘K’ [-Wunused-variable]
int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
^
xCNV.c: In function ‘baum_welch’:
xCNV.c:787:20: warning: unused variable ‘sd_b_tmp’ [-Wunused-variable]
double mu_b_tmp, sd_b_tmp;
^
xCNV.c:787:10: warning: unused variable ‘mu_b_tmp’ [-Wunused-variable]
double mu_b_tmp, sd_b_tmp;
^
xCNV.c:762:10: warning: variable ‘LL’ set but not used [-Wunused-but-set-variable]
int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
^
xCNV.c:1839:24: warning: ‘pbf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
^
xCNV.c:1839:24: warning: ‘nGtp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o genoCN.so tnorm_mle.o utility.o xCNV.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/genoCN.Rcheck/genoCN/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genoCN)