Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 925/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Harshlight 1.77.0 (landing page) Maurizio Pellegrino
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.77.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Harshlight.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Harshlight_1.77.0.tar.gz |
StartedAt: 2024-08-21 01:35:00 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 01:36:41 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 100.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Harshlight.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Harshlight.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Harshlight_1.77.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Harshlight.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'Harshlight/DESCRIPTION' ... OK * this is package 'Harshlight' version '1.77.0' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'Harshlight' can be installed ... WARNING Found the following significant warnings: Harshlight.c:1471:26: warning: unknown conversion type character ')' in format [-Wformat=] Harshlight.c:1474:26: warning: unknown conversion type character ')' in format [-Wformat=] Harshlight.c:1532:107: warning: unknown conversion type character ')' in format [-Wformat=] Harshlight.c:1542:26: warning: unknown conversion type character ')' in format [-Wformat=] Harshlight.c:1543:26: warning: unknown conversion type character ')' in format [-Wformat=] Harshlight.c:1555:107: warning: unknown conversion type character ')' in format [-Wformat=] See 'F:/biocbuild/bbs-3.20-bioc/meat/Harshlight.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Calls with DUP: .C("cluster_defects", img <- as.integer(img), array.size <- as.integer(array.size), as.integer(size.limit), as.integer(connect), as.double(simul.pval), as.double(compact.pval), as.integer(type), status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight") .C("diffuse_defects", img <- as.double(img), as.double(diffuse.bright), as.double(-diffuse.dark), as.integer(radius), diff.bright <- as.double(diff.bright), diff.dark <- as.double(diff.dark), as.double(quant), as.double(thres.dark), as.double(thres.bright), status <- as.integer(0), DUP = FALSE, NAOK = TRUE, PACKAGE = "Harshlight") .C("extended_defects", as.double(img), med.obs <- as.double(med.obs), as.integer(radius), status <- as.integer(0), NAOK = TRUE, DUP = FALSE, PACKAGE = "Harshlight") .C("image_dilation", as.double(img), result <- as.double(result), as.integer(radius), status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight") .C("image_erosion", as.double(result), img <- as.double(img), as.integer(radius), status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight") .C("simulations", simulation.bright <- as.integer(simulation.bright), as.double(compact.quant.bright), as.integer(compact.connect), status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight") .C("simulations", simulation.dark <- as.integer(simulation.dark), as.double(compact.quant.dark), as.integer(compact.connect), status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight") DUP is no longer supported and will be ignored. * checking R code for possible problems ... NOTE Harshlight: no visible binding for global variable 'sim' Harshlight: no visible binding for global variable 'sim.int' Undefined global functions or variables: sim sim.int * checking Rd files ... NOTE checkRd: (-1) sim.Rd:10: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/Harshlight/libs/x64/Harshlight.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'rand', possibly from 'rand' (C) Found 'srand', possibly from 'srand' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/Harshlight.Rcheck/00check.log' for details.
Harshlight.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Harshlight ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'Harshlight' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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:1471:26: warning: unknown conversion type character ')' in format [-Wformat=] 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: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=] 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:1532:107: warning: unknown conversion type character ')' in format [-Wformat=] 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:1542:26: warning: unknown conversion type character ')' in format [-Wformat=] 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: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=] 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); | ^ Harshlight.c:1555:107: warning: unknown conversion type character ')' in format [-Wformat=] gcc -shared -s -static-libgcc -o Harshlight.dll tmp.def Harshlight.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-Harshlight/00new/Harshlight/libs/x64 ** R ** data ** 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 (Harshlight)
Harshlight.Rcheck/Harshlight-Ex.timings
name | user | system | elapsed | |
Harshlight | 0 | 0 | 0 | |