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INSTALL report for methylKit on malbec1

This page was generated on 2021-05-06 12:28:13 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the methylKit package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1077/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylKit 1.16.1  (landing page)
Altuna Akalin , Alexander Gosdschan
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/methylKit
Branch: RELEASE_3_12
Last Commit: a48c559
Last Changed Date: 2021-01-28 09:43:19 -0400 (Thu, 28 Jan 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: methylKit
Version: 1.16.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL methylKit
StartedAt: 2021-05-05 16:40:20 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 16:41:25 -0400 (Wed, 05 May 2021)
EllapsedTime: 64.9 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL methylKit
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘methylKit’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c methCall.cpp -o methCall.o
methCall.cpp: In function ‘int process_single_bismark(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, size_t&)’:
methCall.cpp:1244:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1243:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1242:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function ‘int process_sam(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, int, size_t&)’:
methCall.cpp:687:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:686:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:685:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function ‘int process_bam(std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, size_t&)’:
methCall.cpp:1014:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1013:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1012:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o /home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-methylKit/00new/methylKit/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (methylKit)