tweeDEseq 1.3.0
Juan R Gonzalez
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/tweeDEseq | | Last Changed Rev: 64680 / Revision: 66885 | | Last Changed Date: 2012-03-30 15:15:56 -0700 (Fri, 30 Mar 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | ERROR | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | ERROR | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/tweeDEseq.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'tweeDEseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tweeDEseq' version '1.3.0'
* 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 whether package 'tweeDEseq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... ERROR
Running examples in 'tweeDEseq-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: normalizeCounts
> ### Title: Count data normalization
> ### Aliases: normalizeCounts
> ### Keywords: misc
>
> ### ** Examples
>
> # Generate a random matrix of counts
> counts <- matrix(rPT(n=1000, a=0.5, mu=10, D=5), ncol = 40)
>
> colSums(counts)
[1] 275 236 216 259 280 240 222 284 260 214 207 187 277 291 248 241 306 242 250
[20] 231 260 292 250 261 276 268 243 226 252 202 271 269 290 248 227 231 235 276
[39] 276 258
> counts[1:5, 1:5]
[,1] [,2] [,3] [,4] [,5]
[1,] 5 7 8 19 11
[2,] 7 1 17 17 6
[3,] 9 7 7 7 5
[4,] 20 17 5 14 37
[5,] 4 6 2 25 11
>
> # Normalize counts
> normCounts <- normalizeCounts(counts, rep(c(1,2), 20))
Using edgeR-TMM normalization.
Calculating normalization factors with the TMM method.
Estimating common dispersion.
Estimating tagwise dispersions.
Calculating effective library sizes.
Adjusting counts to effective library sizes using tagwise dispersions.
Error in edgeR::equalizeLibSizes(d2, disp = dispersion, null.hypothesis = TRUE) :
unused argument(s) (null.hypothesis = TRUE)
Calls: normalizeCounts -> <Anonymous>
Execution halted
* installing *source* package 'tweeDEseq' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c cov_wt_C.c -o cov_wt_C.o
cov_wt_C.c: In function 'momentEstimates_wt_C':
cov_wt_C.c:116: warning: 'moments' may be used uninitialized in this function
cov_wt_C.c: In function 'cov_wt_C':
cov_wt_C.c:49: warning: 'wvar' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c init_tweeDEseq.c -o init_tweeDEseq.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c loglikGlm.c -o loglikGlm.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c permtest.c -o permtest.o
permtest.c: In function 'pval':
permtest.c:43: warning: control reaches end of non-void function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c probs.c -o probs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c zhu2.c -o zhu2.o
zhu2.c: In function 'zhuprobs':
zhu2.c:30: warning: ordered comparison of pointer with integer zero
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c zhu3.c -o zhu3.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o tweeDEseq.so cov_wt_C.o init_tweeDEseq.o loglikGlm.o permtest.o probs.o zhu2.o zhu3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/tweeDEseq.Rcheck/tweeDEseq/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'tweeDEseq.Rnw' using 'UTF-8'
** testing if installed package can be loaded
* DONE (tweeDEseq)