Jan Janecka
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/chromDraw |
| git_branch: master |
| git_last_commit: 8c2daf3 |
| git_last_commit_date: 2021-10-26 12:18:12 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:11 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 308/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chromDraw 2.25.0 (landing page) Jan Janecka
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: chromDraw |
| Version: 2.25.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL chromDraw |
| StartedAt: 2022-03-17 15:39:14 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 15:40:48 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 94.1 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL chromDraw
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'chromDraw' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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>' is used uninitialized in this function [-Wuninitialized]
Point( const Point & other ):x(other.x),y(other.y) { }
~~~~~~^
./libBoard/include/board/Point.h:71:51: warning: '*((void*)&<anonymous> +8)' is used uninitialized in this function [-Wuninitialized]
Point( const Point & other ):x(other.x),y(other.y) { }
~~~~~~^
./libBoard/include/board/Point.h:71:40: warning: '<anonymous>' is used uninitialized in this function [-Wuninitialized]
Point( const Point & other ):x(other.x),y(other.y) { }
~~~~~~^
./libBoard/include/board/Point.h:71:51: warning: '*((void*)&<anonymous> +8)' is used uninitialized in this function [-Wuninitialized]
Point( const Point & other ):x(other.x),y(other.y) { }
~~~~~~^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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]
strncpy( str, ctime(t), count );
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c libBoard/src/Path.cpp -o libBoard/src/Path.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c libBoard/src/Color.cpp -o libBoard/src/Color.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
"C:/rtools40/mingw64/bin/"ar crs libSn1.a libBoard/src/Shapes.o libBoard/src/Tools.o libBoard/src/Board.o libBoard/src/Transforms.o libBoard/src/Rect.o libBoard/src/ShapeList.o libBoard/src/Path.o libBoard/src/Color.o libBoard/src/PSFonts.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o
chromDrawCPP/parameters.cpp:66:21: warning: extra tokens at end of #ifdef directive
#ifdef _WIN32 || _WIN64
^~
chromDrawCPP/parameters.cpp:147:15: warning: extra tokens at end of #ifdef directive
#ifdef _WIN32 || _WIN64
^~
chromDrawCPP/parameters.cpp:159:15: warning: extra tokens at end of #ifdef directive
#ifdef _WIN32 || _WIN64
^~
chromDrawCPP/parameters.cpp: In member function 'int parameters::loadArguments(int, char**)':
chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
"--format"};
^
chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o
chromDrawCPP/ideogram.cpp: In member function 'int ideogram::loadMatrix(std::__cxx11::string, std::__cxx11::string)':
chromDrawCPP/ideogram.cpp:80:2: warning: 'retVal' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(retVal != 0)
^~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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]
char x = argv[argcurent][1];
^
chromDrawCPP/getOpts.cpp:48:8: warning: unused variable 'y' [-Wunused-variable]
char y = argv[argcurent][2];
^
chromDrawCPP/getOpts.cpp:49:8: warning: unused variable 'o' [-Wunused-variable]
char o = optv[optcurent];
^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:320:8: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized]
float coordinate_y;
^~~~~~~~~~~~
chromDrawCPP/canvas.cpp: In member function 'void canvas::lin_drawEllipseMarkSign(int, canvas::ELocationOnChromosome, int)':
chromDrawCPP/canvas.cpp:396:8: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized]
float coordinate_y;
^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o
chromDrawCPP/karyotype.cpp: In member function 'int karyotype::loadMatrix(std::ifstream*)':
chromDrawCPP/karyotype.cpp:266:14: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
delete block;
^~~~~
chromDrawCPP/karyotype.cpp:274:13: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
delete block;
^~~~~
chromDrawCPP/karyotype.cpp:315:13: warning: deleting object of polymorphic class type 'chCentromere' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
delete centromere;
^~~~~~~~~~
chromDrawCPP/karyotype.cpp:421:14: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
delete mark;
^~~~
chromDrawCPP/karyotype.cpp:429:13: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
delete mark;
^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
"C:/rtools40/mingw64/bin/"ar crs libSn2.a chromDrawCPP/chromosomeMark.o chromDrawCPP/chromosomeElement.o chromDrawCPP/parameters.o chromDrawCPP/colorPalette.o chromDrawCPP/chromosomeSign.o chromDrawCPP/ideogram.o chromDrawCPP/chBlock.o chromDrawCPP/getOpts.o chromDrawCPP/markSign.o chromDrawCPP/chromosome.o chromDrawCPP/canvas.o chromDrawCPP/color.o chromDrawCPP/karyotype.o chromDrawCPP/chCentromere.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chromDraw.cpp -o chromDraw.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_init_chromDraw.cpp -o R_init_chromDraw.o
"C:/rtools40/mingw64/bin/"ar crs libSn3.a RcppExports.o chromDraw.o R_init_chromDraw.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o chromDraw.dll tmp.def chromDraw.o RcppExports.o libSn1.a libSn2.a libSn3.a -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-chromDraw/00new/chromDraw/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'chromDraw'
finding HTML links ... done
chromDraw-package html
chromDraw html
chromDrawGR html
convertInputColors html
convertInputData html
main_chromDraw html
** 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)
Making 'packages.html' ... done