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This page was generated on 2023-02-07 11:05:07 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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INSTALL results for chromDraw on nebbiolo1


To the developers/maintainers of the chromDraw package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromDraw.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 316/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromDraw 2.29.0  (landing page)
Jan Janecka
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/chromDraw
git_branch: master
git_last_commit: 607aea8
git_last_commit_date: 2022-11-01 11:10:54 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: chromDraw
Version: 2.29.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL chromDraw
StartedAt: 2023-02-06 15:09:33 -0500 (Mon, 06 Feb 2023)
EndedAt: 2023-02-06 15:10:13 -0500 (Mon, 06 Feb 2023)
EllapsedTime: 40.1 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL chromDraw
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘chromDraw’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDraw.cpp -o chromDraw.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c libBoard/src/Board.cpp -o libBoard/src/Board.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c libBoard/src/Color.cpp -o libBoard/src/Color.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c libBoard/src/Path.cpp -o libBoard/src/Path.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/canvas.cpp -o chromDrawCPP/canvas.o
chromDrawCPP/canvas.cpp: In member function ‘void canvas::lin_drawRectangleMarkSign(int, canvas::ELocationOnChromosome, int)’:
chromDrawCPP/canvas.cpp:369:68: warning: ‘coordinate_y’ may be used uninitialized [-Wmaybe-uninitialized]
  369 |         sheet.drawRectangle(last_x-0.5*sizefactor*MARK_WIDTHSIZE1, coordinate_y+0.5*sizefactor*MARK_HEIGHTSIZE1, sizefactor*MARK_WIDTHSIZE1, sizefactor*MARK_HEIGHTSIZE1);
      |                                                                    ^~~~~~~~~~~~
chromDrawCPP/canvas.cpp: In member function ‘void canvas::lin_drawEllipseMarkSign(int, canvas::ELocationOnChromosome, int)’:
chromDrawCPP/canvas.cpp:446:26: warning: ‘coordinate_y’ may be used uninitialized [-Wmaybe-uninitialized]
  446 |         sheet.drawEllipse(last_x,coordinate_y, sizefactor*MARK_WIDTHSIZE1/2.0,sizefactor*MARK_HEIGHTSIZE1);
      |         ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/getOpts.cpp -o chromDrawCPP/getOpts.o
chromDrawCPP/getOpts.cpp: In member function ‘char getOpts::getOptions(int, char**, char*, char**)’:
chromDrawCPP/getOpts.cpp:47:22: warning: unused variable ‘x’ [-Wunused-variable]
   47 |                 char x = argv[argcurent][1];
      |                      ^
chromDrawCPP/getOpts.cpp:48:22: warning: unused variable ‘y’ [-Wunused-variable]
   48 |                 char y = argv[argcurent][2];
      |                      ^
chromDrawCPP/getOpts.cpp:49:22: warning: unused variable ‘o’ [-Wunused-variable]
   49 |                 char o = optv[optcurent];
      |                      ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o
chromDrawCPP/ideogram.cpp: In member function ‘int ideogram::loadMatrix(std::string, std::string)’:
chromDrawCPP/ideogram.cpp:70:13: warning: ‘retVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   70 |         int retVal;
      |             ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o
chromDrawCPP/karyotype.cpp: In member function ‘int karyotype::loadMatrix(std::ifstream*)’:
chromDrawCPP/karyotype.cpp:266:49: warning: deleting object of polymorphic class type ‘chBlock’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
  266 |                                                 delete block;
      |                                                 ^~~~~~~~~~~~
chromDrawCPP/karyotype.cpp:274:41: warning: deleting object of polymorphic class type ‘chBlock’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
  274 |                                         delete block;
      |                                         ^~~~~~~~~~~~
chromDrawCPP/karyotype.cpp:315:41: warning: deleting object of polymorphic class type ‘chCentromere’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
  315 |                                         delete centromere;
      |                                         ^~~~~~~~~~~~~~~~~
chromDrawCPP/karyotype.cpp:421:49: warning: deleting object of polymorphic class type ‘markSign’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
  421 |                                                 delete mark;
      |                                                 ^~~~~~~~~~~
chromDrawCPP/karyotype.cpp:429:41: warning: deleting object of polymorphic class type ‘markSign’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
  429 |                                         delete mark;
      |                                         ^~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o
chromDrawCPP/parameters.cpp:66:63: warning: extra tokens at end of #ifdef directive
   66 |                                                 #ifdef _WIN32 || _WIN64
      |                                                               ^~
chromDrawCPP/parameters.cpp:147:15: warning: extra tokens at end of #ifdef directive
  147 | #ifdef _WIN32 || _WIN64
      |               ^~
chromDrawCPP/parameters.cpp:159:15: warning: extra tokens at end of #ifdef directive
  159 | #ifdef _WIN32 || _WIN64
      |               ^~
chromDrawCPP/parameters.cpp: In member function ‘int parameters::loadArguments(int, char**)’:
chromDrawCPP/parameters.cpp:42:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   42 |         char *paramsExpanded[10] = {"--help",
      |                                     ^~~~~~~~
chromDrawCPP/parameters.cpp:43:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   43 |                                                                 "--outputpath",
      |                                                                 ^~~~~~~~~~~~~~
chromDrawCPP/parameters.cpp:44:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   44 |                                                                 "--colorinputpath",
      |                                                                 ^~~~~~~~~~~~~~~~~~
chromDrawCPP/parameters.cpp:45:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   45 |                                                                 "--datainputpath",
      |                                                                 ^~~~~~~~~~~~~~~~~
chromDrawCPP/parameters.cpp:46:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   46 |                                                                 "--scale",
      |                                                                 ^~~~~~~~~
chromDrawCPP/parameters.cpp:47:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   47 |                                                                 "--format"};
      |                                                                 ^~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_chromDraw.cpp -o R_init_chromDraw.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o chromDraw.so chromDraw.o RcppExports.o ./libBoard/src/Board.o ./libBoard/src/Color.o ./libBoard/src/PSFonts.o ./libBoard/src/Path.o ./libBoard/src/Rect.o ./libBoard/src/ShapeList.o ./libBoard/src/Shapes.o ./libBoard/src/Tools.o ./libBoard/src/Transforms.o ./chromDrawCPP/canvas.o ./chromDrawCPP/chBlock.o ./chromDrawCPP/chCentromere.o ./chromDrawCPP/chromosome.o ./chromDrawCPP/chromosomeElement.o ./chromDrawCPP/chromosomeMark.o ./chromDrawCPP/chromosomeSign.o ./chromDrawCPP/color.o ./chromDrawCPP/colorPalette.o ./chromDrawCPP/getOpts.o ./chromDrawCPP/ideogram.o ./chromDrawCPP/karyotype.o ./chromDrawCPP/markSign.o ./chromDrawCPP/parameters.o ./R_init_chromDraw.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-chromDraw/00new/chromDraw/libs
** R
** 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 (chromDraw)