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INSTALL report for Harshlight on tokay2

This page was generated on 2020-10-17 11:56:48 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Harshlight PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 802/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Harshlight 1.60.0
Maurizio Pellegrino
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Harshlight
Branch: RELEASE_3_11
Last Commit: 30e3612
Last Changed Date: 2020-04-27 14:13:34 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Harshlight
Version: 1.60.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Harshlight_1.60.0.tar.gz && rm -rf Harshlight.buildbin-libdir && mkdir Harshlight.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Harshlight.buildbin-libdir Harshlight_1.60.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Harshlight_1.60.0.zip && rm Harshlight_1.60.0.tar.gz Harshlight_1.60.0.zip
StartedAt: 2020-10-16 18:43:07 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 18:43:52 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 44.6 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Harshlight_1.60.0.tar.gz && rm -rf Harshlight.buildbin-libdir && mkdir Harshlight.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Harshlight.buildbin-libdir Harshlight_1.60.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Harshlight_1.60.0.zip && rm Harshlight_1.60.0.tar.gz Harshlight_1.60.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  101k  100  101k    0     0  1494k      0 --:--:-- --:--:-- --:--:-- 1667k

install for i386

* installing *source* package 'Harshlight' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Harshlight.c -o Harshlight.o
Harshlight.c: In function 'extended_defects':
Harshlight.c:564:20: warning: variable 'p_num_points' set but not used [-Wunused-but-set-variable]
   int num_points, *p_num_points; //number of points inside the median kernel
                    ^~~~~~~~~~~~
Harshlight.c: In function 'image_dilation':
Harshlight.c:948:10: warning: variable 'cell_value' set but not used [-Wunused-but-set-variable]
   double cell_value;
          ^~~~~~~~~~
Harshlight.c: In function 'norm':
Harshlight.c:1316:27: warning: unused variable 'sorted2' [-Wunused-variable]
   double *sorted; double *sorted2;
                           ^~~~~~~
Harshlight.c: In function 'report_overall_header':
Harshlight.c:1471:26: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 215, *diff_br);
                          ^
Harshlight.c:1471:26: warning: unknown conversion type character ')' in format [-Wformat=]
Harshlight.c:1474:26: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 230, *diff_dr);
                          ^
Harshlight.c:1474:26: warning: unknown conversion type character ')' in format [-Wformat=]
Harshlight.c: In function 'chip_summary':
Harshlight.c:1532:107: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (Extended defects: the variance of the Error Image explained by the background is %.2f%) show\n", x_text, y_text - 30, *var);
                                                                                                           ^
Harshlight.c:1532:107: warning: unknown conversion type character ')' in format [-Wformat=]
Harshlight.c:1542:26: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (%.2f%) show\n", x_val_1, y_text - 100, *perc_c);
                          ^
Harshlight.c:1542:26: warning: unknown conversion type character ')' in format [-Wformat=]
Harshlight.c:1543:26: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (%.2f%) show\n", x_val_2, y_text - 100, *perc_d);
                          ^
Harshlight.c:1543:26: warning: unknown conversion type character ')' in format [-Wformat=]
Harshlight.c: In function 'extended_stop':
Harshlight.c:1555:107: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (Extended defects: the variance of the Error Image explained by the background is %.2f%) show\n", x_text, y_text - 30, *var);
                                                                                                           ^
Harshlight.c:1555:107: warning: unknown conversion type character ')' in format [-Wformat=]
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o Harshlight.dll tmp.def Harshlight.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/Harshlight.buildbin-libdir/00LOCK-Harshlight/00new/Harshlight/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Harshlight'
    finding HTML links ... done
    HarshComp                               html  
    HarshExt                                html  
    Harshlight                              html  
    sim                                     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

install for x64

* installing *source* package 'Harshlight' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Harshlight.c -o Harshlight.o
Harshlight.c: In function 'extended_defects':
Harshlight.c:564:20: warning: variable 'p_num_points' set but not used [-Wunused-but-set-variable]
   int num_points, *p_num_points; //number of points inside the median kernel
                    ^~~~~~~~~~~~
Harshlight.c: In function 'image_dilation':
Harshlight.c:948:10: warning: variable 'cell_value' set but not used [-Wunused-but-set-variable]
   double cell_value;
          ^~~~~~~~~~
Harshlight.c: In function 'norm':
Harshlight.c:1316:27: warning: unused variable 'sorted2' [-Wunused-variable]
   double *sorted; double *sorted2;
                           ^~~~~~~
Harshlight.c: In function 'report_overall_header':
Harshlight.c:1471:26: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 215, *diff_br);
                          ^
Harshlight.c:1471:26: warning: unknown conversion type character ')' in format [-Wformat=]
Harshlight.c:1474:26: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 230, *diff_dr);
                          ^
Harshlight.c:1474:26: warning: unknown conversion type character ')' in format [-Wformat=]
Harshlight.c: In function 'chip_summary':
Harshlight.c:1532:107: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (Extended defects: the variance of the Error Image explained by the background is %.2f%) show\n", x_text, y_text - 30, *var);
                                                                                                           ^
Harshlight.c:1532:107: warning: unknown conversion type character ')' in format [-Wformat=]
Harshlight.c:1542:26: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (%.2f%) show\n", x_val_1, y_text - 100, *perc_c);
                          ^
Harshlight.c:1542:26: warning: unknown conversion type character ')' in format [-Wformat=]
Harshlight.c:1543:26: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (%.2f%) show\n", x_val_2, y_text - 100, *perc_d);
                          ^
Harshlight.c:1543:26: warning: unknown conversion type character ')' in format [-Wformat=]
Harshlight.c: In function 'extended_stop':
Harshlight.c:1555:107: warning: unknown conversion type character ')' in format [-Wformat=]
   PP "%d %d moveto (Extended defects: the variance of the Error Image explained by the background is %.2f%) show\n", x_text, y_text - 30, *var);
                                                                                                           ^
Harshlight.c:1555:107: warning: unknown conversion type character ')' in format [-Wformat=]
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o Harshlight.dll tmp.def Harshlight.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/Harshlight.buildbin-libdir/Harshlight/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Harshlight' as Harshlight_1.60.0.zip
* DONE (Harshlight)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Harshlight' successfully unpacked and MD5 sums checked