Jan Janecka
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/chromDraw |
| git_branch: RELEASE_3_16 |
| git_last_commit: 6922aac |
| git_last_commit_date: 2022-11-01 11:10:54 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:28 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
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. |
| Package 321/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chromDraw 2.28.0 (landing page) Jan Janecka
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: chromDraw |
| Version: 2.28.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL chromDraw |
| StartedAt: 2023-04-10 15:42:51 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 15:43:46 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 54.9 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL chromDraw
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'chromDraw' ...
** using staged installation
** libs
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Board.cpp -o libBoard/src/Board.o
In file included from ./libBoard/include/board/Tools.h:102,
from ./libBoard/include/board/Shapes.h:51,
from ./libBoard/include/Board.h:51,
from libBoard/src/Board.cpp:43:
In function 'void LibBoard::secured_ctime(char*, const time_t*, size_t)',
inlined from 'void LibBoard::Board::saveEPS(const char*, double, double, double) const' at libBoard/src/Board.cpp:760:18:
./libBoard/include/board/Tools.ih:27:10: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 255 equals destination size [-Wstringop-truncation]
27 | strncpy( str, ctime(t), count );
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Color.cpp -o libBoard/src/Color.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Path.cpp -o libBoard/src/Path.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
In file included from ./libBoard/include/board/Rect.h:46,
from libBoard/src/Shapes.cpp:42:
./libBoard/include/board/Point.h: In member function 'virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)':
./libBoard/include/board/Point.h:71:40: warning: '<anonymous>.LibBoard::Point::x' is used uninitialized in this function [-Wuninitialized]
71 | Point( const Point & other ):x(other.x),y(other.y) { }
| ~~~~~~^
./libBoard/include/board/Point.h:71:51: warning: '<anonymous>.LibBoard::Point::y' is used uninitialized in this function [-Wuninitialized]
71 | Point( const Point & other ):x(other.x),y(other.y) { }
| ~~~~~~^
./libBoard/include/board/Point.h:71:40: warning: '<anonymous>.LibBoard::Point::x' is used uninitialized in this function [-Wuninitialized]
71 | Point( const Point & other ):x(other.x),y(other.y) { }
| ~~~~~~^
./libBoard/include/board/Point.h:71:51: warning: '<anonymous>.LibBoard::Point::y' is used uninitialized in this function [-Wuninitialized]
71 | Point( const Point & other ):x(other.x),y(other.y) { }
| ~~~~~~^
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
ar crs libSn1.a 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
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o
chromDrawCPP/ideogram.cpp: In member function 'int ideogram::loadMatrix(std::string, std::string)':
chromDrawCPP/ideogram.cpp:80:2: warning: 'retVal' may be used uninitialized in this function [-Wmaybe-uninitialized]
80 | if(retVal != 0)
| ^~
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"};
| ^~~~~~~~~~
ar crs libSn2.a 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
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_chromDraw.cpp -o R_init_chromDraw.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDraw.cpp -o chromDraw.o
ar crs libSn3.a R_init_chromDraw.o RcppExports.o chromDraw.o
g++ -std=gnu++14 -shared -s -static-libgcc -o chromDraw.dll tmp.def chromDraw.o RcppExports.o libSn1.a libSn2.a libSn3.a -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-chromDraw/00new/chromDraw/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (chromDraw)