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Package 465/516HostnameOS / ArchBUILDCHECKBUILD BIN
snapCGH 1.24.0
John Marioni
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/snapCGH
Last Changed Rev: 59920 / Revision: 61898
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  ERROR 

Summary

Package: snapCGH
Version: 1.24.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch snapCGH_1.24.0.tar.gz
StartedAt: 2012-01-09 05:45:01 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 05:47:08 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 126.9 seconds
RetCode: 0
Status:  OK  
CheckDir: snapCGH.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/snapCGH.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.24.0'
* 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 'snapCGH' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 ... NOTE
generate.data: no visible binding for global variable
  'zero.length.distr.non.tiled'
generate.data: no visible binding for global variable
  'non.zero.length.distr.non.tiled'
generate.data: no visible binding for global variable
  'zero.length.distr.tiled'
generate.data: no visible binding for global variable
  'non.zero.length.distr.tiled'
heatmapGenome: no visible binding for global variable 'floor.func'
readPositionalInfo: no visible binding for global variable 'RGList'
simulateData: no visible binding for global variable
  'zero.length.distr.non.tiled'
simulateData: no visible binding for global variable
  'zero.length.distr.tiled'
simulateData: no visible binding for global variable
  'non.zero.length.distr.non.tiled'
simulateData: no visible binding for global variable
  'non.zero.length.distr.tiled'
* checking Rd files ... NOTE
prepare_Rd: genomePlot.Rd:51-57: Dropping empty section \examples
prepare_Rd: heatmapGenome.Rd:76-77: Dropping empty section \examples
prepare_Rd: plotSegmentedGenome.Rd:52-58: Dropping empty section \examples
prepare_Rd: sim.structure.Rd:57-58: Dropping empty section \examples
* 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 examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

snapCGH.Rcheck/00install.out:

* installing *source* package 'snapCGH' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3'
optimizer.c:26:23: warning: unused variable 'temp2'
optimizer.c:26:10: warning: unused variable 'denom'
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3'
optimizer.c:195:23: warning: unused variable 'temp2'
optimizer.c:195:10: warning: unused variable 'denom'
optimizer.c:194:69: warning: unused variable 'alphahat'
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3'
optimizer.c:413:23: warning: unused variable 'temp2'
optimizer.c:413:10: warning: unused variable 'denom'
optimizer.c:412:69: warning: unused variable 'alphahat'
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3'
optimizer.c:687:23: warning: unused variable 'temp2'
optimizer.c:687:10: warning: unused variable 'denom'
optimizer.c:686:69: warning: unused variable 'alphahat'
optimizer.c:686:38: warning: 'gammaC[0][0]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[0][1]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[0][2]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[0][3]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[0][4]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[1][0]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[1][1]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[1][2]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[1][3]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[1][4]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[2][0]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[2][1]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[2][2]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[2][3]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[2][4]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[3][0]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[3][1]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[3][2]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[3][3]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[3][4]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[4][0]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[4][1]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[4][2]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[4][3]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[4][4]' may be used uninitialized in this function
optimizer.c:943:4: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false
optimizer.c: In function 'fr_four':
optimizer.c:412:38: warning: 'gammaC[0][0]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[0][1]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[0][2]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[0][3]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[1][0]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[1][1]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[1][2]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[1][3]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[2][0]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[2][1]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[2][2]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[2][3]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[3][0]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[3][1]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[3][2]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[3][3]' may be used uninitialized in this function
optimizer.c:585:1: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false
optimizer.c: In function 'fr_three':
optimizer.c:194:38: warning: 'gammaC[0][0]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[0][1]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[0][2]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[1][0]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[1][1]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[1][2]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[2][0]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[2][1]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[2][2]' may be used uninitialized in this function
optimizer.c: In function 'fr_two':
optimizer.c:25:38: warning: 'gammaC[0][0]' may be used uninitialized in this function
optimizer.c:25:38: warning: 'gammaC[0][1]' may be used uninitialized in this function
optimizer.c:25:38: warning: 'gammaC[1][0]' may be used uninitialized in this function
optimizer.c:25:38: warning: 'gammaC[1][1]' may be used uninitialized in this function
gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/snapCGH.Rcheck/snapCGH/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'snapCGHguide.Rnw' 
** testing if installed package can be loaded

* DONE (snapCGH)

snapCGH.Rcheck/snapCGH-Ex.timings:

nameusersystemelapsed
LargeDataObject000
convert.output000
dim000