CSSP 1.1.2
Chandler Zuo
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/CSSP | | Last Changed Rev: 87237 / Revision: 88450 | | Last Changed Date: 2014-03-08 12:31:09 -0800 (Sat, 08 Mar 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/CSSP.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 ‘CSSP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSSP’ version ‘1.1.2’
* 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 ‘CSSP’ can be installed ... [3s/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 ... NOTE
Namespaces in Imports field not imported from:
‘methods’ ‘stats’ ‘utils’
All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
cssp.power-methods 29.554 0.068 29.696
cssp.fit-methods 6.456 0.008 6.476
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘run_tests.R’ [4s/4s]
[4s/4s] 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
NOTE: There was 1 note.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/CSSP.Rcheck/00check.log’
for details.
* installing *source* package ‘CSSP’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bincount.c -o bincount.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c binpower.c -o binpower.o
binpower.c: In function ‘binpower’:
binpower.c:72:2: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
binpower.c:105:2: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
binpower.c: In function ‘binpower_pval’:
binpower.c:162:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
binpower.c:141:30: warning: unused variable ‘tmp’ [-Wunused-variable]
binpower.c:141:10: warning: unused variable ‘sim_bin’ [-Wunused-variable]
binpower.c:136:40: warning: unused variable ‘rscale_back’ [-Wunused-variable]
binpower.c:136:11: warning: unused variable ‘rsize_back’ [-Wunused-variable]
binpower.c:135:34: warning: unused variable ‘k’ [-Wunused-variable]
binpower.c: In function ‘binpower’:
binpower.c:88:9: warning: ‘p_thre’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gridLogMean.c -o gridLogMean.o
gridLogMean.c: In function ‘gridMGClogmean_c’:
gridLogMean.c:29:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:29:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridLogMean.c:29:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridLogMean.c:29:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:35:4: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridLogMean.c:35:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:35:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:35:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:43:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:45:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridLogMean.c:77:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:77:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:77:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:157:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:157:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:157:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:10:63: warning: unused variable ‘counter’ [-Wunused-variable]
gridLogMean.c: In function ‘gridMlogmean_c’:
gridLogMean.c:193:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridLogMean.c:193:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:199:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:199:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:225:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:295:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridLogMean.c:177:63: warning: unused variable ‘counter’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gridMGC.c -o gridMGC.o
gridMGC.c: In function ‘gridMGC_c’:
gridMGC.c:29:4: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMGC.c:29:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMGC.c:29:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMGC.c:29:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMGC.c:37:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMGC.c:39:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMGC.c:71:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMGC.c:71:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMGC.c:71:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMGC.c: In function ‘gridM_c’:
gridMGC.c:177:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMGC.c:177:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMGC.c:203:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gridMean.c -o gridMean.o
gridMean.c: In function ‘gridMGCmean_c’:
gridMean.c:29:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:29:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMean.c:29:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMean.c:29:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:35:4: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMean.c:35:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:35:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:35:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:43:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:45:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMean.c:77:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:77:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:77:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:157:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:157:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:157:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:10:63: warning: unused variable ‘counter’ [-Wunused-variable]
gridMean.c: In function ‘gridMmean_c’:
gridMean.c:193:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMean.c:193:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:199:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:199:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:225:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:295:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMean.c:177:63: warning: unused variable ‘counter’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gridMode.c -o gridMode.o
gridMode.c: In function ‘gridMGCmode_c’:
gridMode.c:31:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:31:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMode.c:31:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMode.c:31:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:37:4: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMode.c:37:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:37:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:37:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:45:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:47:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMode.c:79:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:79:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:79:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:164:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:164:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:164:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c: In function ‘gridMmode_c’:
gridMode.c:219:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridMode.c:219:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:225:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:225:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:251:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridMode.c:326:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gridNonpa.c -o gridNonpa.o
gridNonpa.c: In function ‘gridMGCnonpa_c’:
gridNonpa.c:29:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:29:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridNonpa.c:29:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridNonpa.c:29:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:35:4: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridNonpa.c:35:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:35:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:35:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:43:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:45:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridNonpa.c:77:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:77:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:77:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:161:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:161:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:161:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:10:63: warning: unused variable ‘counter’ [-Wunused-variable]
gridNonpa.c: In function ‘gridMnonpa_c’:
gridNonpa.c:209:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridNonpa.c:209:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:215:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:215:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:241:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:315:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridNonpa.c:193:62: warning: unused variable ‘counter’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gridSample.c -o gridSample.o
gridSample.c: In function ‘gridMGCsample_c’:
gridSample.c:33:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:33:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridSample.c:33:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridSample.c:33:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:39:4: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridSample.c:39:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:39:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:39:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:47:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:49:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridSample.c:81:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:81:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:81:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:166:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:166:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:166:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c: In function ‘gridMsample_c’:
gridSample.c:224:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gridSample.c:224:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:230:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:230:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:256:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gridSample.c:331:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tag2bin.c -o tag2bin.o
gcc -std=gnu99 -shared -L/usr/local/lib -o CSSP.so bincount.o binpower.o gridLogMean.o gridMGC.o gridMean.o gridMode.o gridNonpa.o gridSample.o tag2bin.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/CSSP.Rcheck/CSSP/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 (CSSP)