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BioC 3.0: INSTALL report for PICS on moscato1

This page was generated on 2015-04-10 09:46:21 -0700 (Fri, 10 Apr 2015).

Package 662/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PICS 2.10.0
Renan Sauteraud
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/PICS
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: PICS
Version: 2.10.0
Command: C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.0/bioc/src/contrib/PICS_2.10.0.tar.gz && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch PICS_2.10.0.tar.gz && rm PICS_2.10.0.tar.gz
StartedAt: 2015-04-09 18:20:14 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 18:21:41 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 87.8 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.0/bioc/src/contrib/PICS_2.10.0.tar.gz && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch PICS_2.10.0.tar.gz && rm PICS_2.10.0.tar.gz
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  819k  100  819k    0     0  37.0M      0 --:--:-- --:--:-- --:--:-- 50.0M

install for i386

* installing to library 'D:/biocbld/bbs-3.0-bioc/R/library'
* installing *source* package 'PICS' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581:25: warning: unused variable 'mu' [-Wunused-variable]
pics.c: In function 'ECM1':
pics.c:803:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
pics.c:963:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
pics.c:651:15: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'ECM2':
pics.c:1009:66: warning: unused variable 'ee' [-Wunused-variable]
pics.c:1009:57: warning: unused variable 'ggR' [-Wunused-variable]
pics.c:1009:52: warning: unused variable 'ggF' [-Wunused-variable]
pics.c:1009:47: warning: unused variable 'aaR' [-Wunused-variable]
pics.c:1009:42: warning: unused variable 'aaF' [-Wunused-variable]
pics.c:1009:29: warning: unused variable 'etaDiff' [-Wunused-variable]
pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
pics.c:1000:15: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'BIC':
pics.c:1272:96: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'getInfMat':
pics.c:1633:76: warning: unused variable 'PhiRw' [-Wunused-variable]
pics.c:1633:69: warning: unused variable 'PhiFw' [-Wunused-variable]
pics.c: In function 'mergePeak':
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable]
pics.c: In function 'BIC':
pics.c:1307:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
pics.c: In function 'fitModelK':
pics.c:421:18: warning: 'firstFit' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:123:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:114:45: warning: unused variable 'count' [-Wunused-variable]
segment.c: In function 'callRegions':
segment.c:308:7: warning: unused variable 'i' [-Wunused-variable]
segment.c: In function 'getSegL':
segment.c:1364:11: warning: unused variable 'j' [-Wunused-variable]
segment.c: In function 'getDensity':
segment.c:1543:9: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1544:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1545:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1546:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1547:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1548:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1549:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable]
segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable]
gcc -m32 -shared -s -static-libgcc -o PICS.dll tmp.def pics.o segment.o -lws2_32 -LC:/GSL/i386/lib -lgsl -lgslcblas -lm -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/R/library/PICS/libs/i386
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: levels, as.factor, elementMetadata, elementMetadata<-
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: levels, as.factor, elementMetadata, elementMetadata<-

install for x64

* installing to library 'D:/biocbld/bbs-3.0-bioc/R/library'
* installing *source* package 'PICS' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581:25: warning: unused variable 'mu' [-Wunused-variable]
pics.c: In function 'ECM1':
pics.c:803:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
pics.c:963:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
pics.c:651:15: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'ECM2':
pics.c:1009:66: warning: unused variable 'ee' [-Wunused-variable]
pics.c:1009:57: warning: unused variable 'ggR' [-Wunused-variable]
pics.c:1009:52: warning: unused variable 'ggF' [-Wunused-variable]
pics.c:1009:47: warning: unused variable 'aaR' [-Wunused-variable]
pics.c:1009:42: warning: unused variable 'aaF' [-Wunused-variable]
pics.c:1009:29: warning: unused variable 'etaDiff' [-Wunused-variable]
pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
pics.c:1000:15: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'BIC':
pics.c:1272:96: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'getInfMat':
pics.c:1633:76: warning: unused variable 'PhiRw' [-Wunused-variable]
pics.c:1633:69: warning: unused variable 'PhiFw' [-Wunused-variable]
pics.c: In function 'mergePeak':
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable]
pics.c: In function 'BIC':
pics.c:1307:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
pics.c: In function 'fitModelK':
pics.c:421:18: warning: 'firstFit' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:123:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:114:45: warning: unused variable 'count' [-Wunused-variable]
segment.c: In function 'callRegions':
segment.c:308:7: warning: unused variable 'i' [-Wunused-variable]
segment.c: In function 'getSegL':
segment.c:1364:11: warning: unused variable 'j' [-Wunused-variable]
segment.c: In function 'getDensity':
segment.c:1543:9: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1544:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1545:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1546:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1547:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1548:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1549:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable]
segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable]
gcc -m64 -shared -s -static-libgcc -o PICS.dll tmp.def pics.o segment.o -lws2_32 -LC:/GSL/x64/lib -lgsl -lgslcblas -lm -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/R/library/PICS/libs/x64
** testing if installed package can be loaded
No methods found in "IRanges" for requests: levels, as.factor, elementMetadata, elementMetadata<-
* DONE (PICS)