Jan Janecka
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024) |
| git_url: https://git.bioconductor.org/packages/chromDraw |
| git_branch: RELEASE_3_19 |
| git_last_commit: 13cf60b |
| git_last_commit_date: 2024-04-30 10:41:01 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:40:40 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 345/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chromDraw 2.34.0 (landing page) Jan Janecka
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the chromDraw package: - 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 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: chromDraw |
| Version: 2.34.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL chromDraw |
| StartedAt: 2024-05-08 20:11:04 -0000 (Wed, 08 May 2024) |
| EndedAt: 2024-05-08 20:12:22 -0000 (Wed, 08 May 2024) |
| EllapsedTime: 77.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL chromDraw
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘chromDraw’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromDraw.cpp -o chromDraw.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c libBoard/src/Board.cpp -o libBoard/src/Board.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c libBoard/src/Color.cpp -o libBoard/src/Color.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c libBoard/src/Path.cpp -o libBoard/src/Path.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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:369:61: warning: ‘coordinate_y’ may be used uninitialized in this function [-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:446:19: warning: ‘coordinate_y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
446 | sheet.drawEllipse(last_x,coordinate_y, sizefactor*MARK_WIDTHSIZE1/2.0,sizefactor*MARK_HEIGHTSIZE1);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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:47:8: warning: unused variable ‘x’ [-Wunused-variable]
47 | char x = argv[argcurent][1];
| ^
chromDrawCPP/getOpts.cpp:48:8: warning: unused variable ‘y’ [-Wunused-variable]
48 | char y = argv[argcurent][2];
| ^
chromDrawCPP/getOpts.cpp:49:8: warning: unused variable ‘o’ [-Wunused-variable]
49 | char o = optv[optcurent];
| ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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:70:6: warning: ‘retVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
70 | int retVal;
| ^~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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:266:7: 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:274:6: 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:315:6: 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:421:7: 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:429:6: 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++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o
chromDrawCPP/parameters.cpp:66:21: 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:42:30: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
42 | char *paramsExpanded[10] = {"--help",
| ^~~~~~~~
chromDrawCPP/parameters.cpp:43:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
43 | "--outputpath",
| ^~~~~~~~~~~~~~
chromDrawCPP/parameters.cpp:44:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
44 | "--colorinputpath",
| ^~~~~~~~~~~~~~~~~~
chromDrawCPP/parameters.cpp:45:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
45 | "--datainputpath",
| ^~~~~~~~~~~~~~~~~
chromDrawCPP/parameters.cpp:46:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
46 | "--scale",
| ^~~~~~~~~
chromDrawCPP/parameters.cpp:47:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
47 | "--format"};
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_chromDraw.cpp -o R_init_chromDraw.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-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)