| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-18 11:41 -0400 (Mon, 18 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 953/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Harshlight 1.80.0 (landing page) Maurizio Pellegrino
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK |  | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the Harshlight package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Harshlight.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. |
| Package: Harshlight |
| Version: 1.80.0 |
| Command: chmod a+r Harshlight -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Harshlight |
| StartedAt: 2025-08-14 19:38:28 -0400 (Thu, 14 Aug 2025) |
| EndedAt: 2025-08-14 19:38:31 -0400 (Thu, 14 Aug 2025) |
| EllapsedTime: 3.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### chmod a+r Harshlight -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Harshlight
###
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* checking for file 'Harshlight/DESCRIPTION' ... OK
* preparing 'Harshlight':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package 'Harshlight' ...
** this is package 'Harshlight' version '1.80.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -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]
564 | 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]
948 | double cell_value;
| ^~~~~~~~~~
Harshlight.c: In function 'norm':
Harshlight.c:1316:27: warning: unused variable 'sorted2' [-Wunused-variable]
1316 | double *sorted; double *sorted2;
| ^~~~~~~
Harshlight.c: In function 'report_overall_header':
Harshlight.c:1471:26: warning: unknown conversion type character ')' in format [-Wformat=]
1471 | PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 215, *diff_br);
| ^
Harshlight.c:1474:26: warning: unknown conversion type character ')' in format [-Wformat=]
1474 | PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 230, *diff_dr);
| ^
Harshlight.c: At top level:
Harshlight.c:1504:6: error: conflicting types for 'chip_overall_header'; have 'void(int *, char **)'
1504 | void chip_overall_header(int *chip_number, char **chip_name){
| ^~~~~~~~~~~~~~~~~~~
Harshlight.c:93:6: note: previous declaration of 'chip_overall_header' with type 'void(void)'
93 | void chip_overall_header(); //general header for a chip
| ^~~~~~~~~~~~~~~~~~~
Harshlight.c: In function 'chip_summary':
Harshlight.c:1532:107: warning: unknown conversion type character ')' in format [-Wformat=]
1532 | 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:1542:26: warning: unknown conversion type character ')' in format [-Wformat=]
1542 | PP "%d %d moveto (%.2f%) show\n", x_val_1, y_text - 100, *perc_c);
| ^
Harshlight.c:1543:26: warning: unknown conversion type character ')' in format [-Wformat=]
1543 | PP "%d %d moveto (%.2f%) show\n", x_val_2, y_text - 100, *perc_d);
| ^
Harshlight.c: In function 'extended_stop':
Harshlight.c:1555:107: warning: unknown conversion type character ')' in format [-Wformat=]
1555 | 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);
| ^
make: *** [E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:289: Harshlight.o] Error 1
ERROR: compilation failed for package 'Harshlight'
* removing 'E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpuiLsUw/Rinstb9a82d732480/Harshlight'
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ERROR: package installation failed