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This page was generated on 2024-04-17 11:36:59 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1228/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylKit 1.28.0  (landing page)
Altuna Akalin , Alexander Blume
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/methylKit
git_branch: RELEASE_3_18
git_last_commit: 42a6cbf
git_last_commit_date: 2023-10-24 10:51:28 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

BUILD BIN results for methylKit on palomino4


To the developers/maintainers of the methylKit package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylKit.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: methylKit
Version: 1.28.0
Command: rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL --build --library=methylKit.buildbin-libdir methylKit_1.28.0.tar.gz
StartedAt: 2024-04-16 07:16:03 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 07:17:38 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 94.8 seconds
RetCode: 0
Status:   OK  
PackageFile: methylKit_1.28.0.zip
PackageFileSize: 6.548 MiB

Command output

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###
### Running command:
###
###   rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL --build --library=methylKit.buildbin-libdir methylKit_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'methylKit' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c methCall.cpp -o methCall.o
methCall.cpp: In function 'int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int, size_t&)':
methCall.cpp:908:17: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare]
  908 |   for (i = 0; i < len_cigar; i++)
      |               ~~^~~~~~~~~~~
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int, size_t&)':
methCall.cpp:687:39: warning: 'CHGout' may be used uninitialized [-Wmaybe-uninitialized]
  687 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:547:24: note: 'CHGout' was declared here
  547 |   FILE *out, *CHHout, *CHGout;
      |                        ^~~~~~
methCall.cpp:686:39: warning: 'CHHout' may be used uninitialized [-Wmaybe-uninitialized]
  686 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:547:15: note: 'CHHout' was declared here
  547 |   FILE *out, *CHHout, *CHGout;
      |               ^~~~~~
methCall.cpp:685:39: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized]
  685 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:547:9: note: 'out' was declared here
  547 |   FILE *out, *CHHout, *CHGout;
      |         ^~~
methCall.cpp: In function 'int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int, size_t&)':
methCall.cpp:1008:39: warning: 'CHGout' may be used uninitialized [-Wmaybe-uninitialized]
 1008 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:827:24: note: 'CHGout' was declared here
  827 |   FILE *out, *CHHout, *CHGout;
      |                        ^~~~~~
methCall.cpp:1007:39: warning: 'CHHout' may be used uninitialized [-Wmaybe-uninitialized]
 1007 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:827:15: note: 'CHHout' was declared here
  827 |   FILE *out, *CHHout, *CHGout;
      |               ^~~~~~
methCall.cpp:1006:39: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized]
 1006 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:827:9: note: 'out' was declared here
  827 |   FILE *out, *CHHout, *CHGout;
      |         ^~~
methCall.cpp: In function 'int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, size_t&)':
methCall.cpp:1238:39: warning: 'CHGout' may be used uninitialized [-Wmaybe-uninitialized]
 1238 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1136:24: note: 'CHGout' was declared here
 1136 |   FILE *out, *CHHout, *CHGout;
      |                        ^~~~~~
methCall.cpp:1237:39: warning: 'CHHout' may be used uninitialized [-Wmaybe-uninitialized]
 1237 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1136:15: note: 'CHHout' was declared here
 1136 |   FILE *out, *CHHout, *CHGout;
      |               ^~~~~~
methCall.cpp:1236:39: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized]
 1236 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1136:9: note: 'out' was declared here
 1136 |   FILE *out, *CHHout, *CHGout;
      |         ^~~
g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/meat/methylKit.buildbin-libdir/00LOCK-methylKit/00new/methylKit/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'methylKit' as methylKit_1.28.0.zip
* DONE (methylKit)