BioC 2.13: CHECK report for iChip on zin1

Package: iChip

Version: 1.16.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings iChip_1.16.0.tar.gz

StartedAt: 2014-04-05 01:56:18 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:56:52 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 34.2 seconds

RetCode: 0

Status:  OK

CheckDir: iChip.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/iChip.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iChip/DESCRIPTION’ ... OK
* this is package ‘iChip’ version ‘1.16.0’
* 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 ‘iChip’ can be installed ... [2s/3s] OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘iChip.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [13s/13s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
iChip2 6.164  0.020   6.197
iChip1 5.840  0.016   5.865
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/iChip.Rcheck/00check.log’
for details.

* installing *source* package ‘iChip’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c iChip.c -o iChip.o
iChip.c: In function ‘iChip2’:
iChip.c:24:69: warning: unused variable ‘sdsignal’ [-Wunused-variable]
iChip.c:24:61: warning: unused variable ‘sdnoise’ [-Wunused-variable]
iChip.c:23:51: warning: variable ‘nrowm1’ set but not used [-Wunused-but-set-variable]
iChip.c: In function ‘iChip1’:
iChip.c:188:20: warning: unused variable ‘j’ [-Wunused-variable]
gcc -std=gnu99 -shared -L/usr/local/lib -o iChip.so iChip.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/iChip.Rcheck/iChip/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iChip)

name	user	system	elapsed
enrichreg	0.016	0.004	0.021
iChip1	5.840	0.016	5.865
iChip2	6.164	0.020	6.197
lmtstat	0.224	0.004	0.229