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 11:42 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 2211/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VegaMC 3.43.0 (landing page) Sandro Morganella
| 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 | WARNINGS | 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 VegaMC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VegaMC.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: VegaMC |
Version: 3.43.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VegaMC.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings VegaMC_3.43.0.tar.gz |
StartedAt: 2024-08-21 06:16:07 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 06:18:14 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 126.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: VegaMC.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VegaMC.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings VegaMC_3.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/VegaMC.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 'VegaMC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'VegaMC' version '3.43.0' * 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 'VegaMC' can be installed ... WARNING Found the following significant warnings: run_vegaMC.c:144:13: warning: too many arguments for format [-Wformat-extra-args] run_vegaMC.c:149:13: warning: too many arguments for format [-Wformat-extra-args] See 'F:/biocbuild/bbs-3.20-bioc/meat/VegaMC.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: example 4.9Mb * 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 ... NOTE Namespace in Imports field not imported from: 'methods' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getGenes: no visible global function definition for 'write.table' qvalue: no visible global function definition for 'smooth.spline' qvalue: no visible global function definition for 'predict' vegaMC,character: no visible global function definition for 'read.table' vegaMC,character: no visible global function definition for 'write.table' Undefined global functions or variables: predict read.table smooth.spline write.table Consider adding importFrom("stats", "predict", "smooth.spline") importFrom("utils", "read.table", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) vegaMC-methods.Rd:55: Lost braces 55 | \item{output_file_name}{(Default code{output}) File name used | ^ * 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 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/VegaMC/libs/x64/VegaMC.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'rand', possibly from 'rand' (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, 5 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/VegaMC.Rcheck/00check.log' for details.
VegaMC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL VegaMC ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'VegaMC' ... ** 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 run_vegaMC.c -o run_vegaMC.o run_vegaMC.c: In function 'run_vegaMC': run_vegaMC.c:144:13: warning: too many arguments for format [-Wformat-extra-args] 144 | Rprintf("\tAberration Matrices Successfully Computed\n", num_seg_regions); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ run_vegaMC.c:149:13: warning: too many arguments for format [-Wformat-extra-args] 149 | Rprintf("\tStatistical Analysis Successfully Completed\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ run_vegaMC.c: In function 'read_params': run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable] 618 | char *elem, *brkt; | ^~~~ run_vegaMC.c: In function 'load_data': run_vegaMC.c:564:14: warning: 'first_probe' may be used uninitialized [-Wmaybe-uninitialized] 564 | prev_chr = temp_probe->chromosome; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ run_vegaMC.c:481:12: note: 'first_probe' was declared here 481 | probe *first_probe, *prev_probe, *temp_probe; | ^~~~~~~~~~~ run_vegaMC.c:535:30: warning: 'position' may be used uninitialized [-Wmaybe-uninitialized] 535 | temp_probe->position = position; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ run_vegaMC.c:498:20: note: 'position' was declared here 498 | int i = 0, position, chr; | ^~~~~~~~ run_vegaMC.c:534:32: warning: 'chr' may be used uninitialized [-Wmaybe-uninitialized] 534 | temp_probe->chromosome = chr; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ run_vegaMC.c:498:30: note: 'chr' was declared here 498 | int i = 0, position, chr; | ^~~ run_vegaMC.c: In function 'call_VegaMC': run_vegaMC.c:435:32: warning: 'prev_seg' may be used uninitialized [-Wmaybe-uninitialized] 435 | prev_seg->next = tmp; | ~~~~~~~~~~~~~~~^~~~~ run_vegaMC.c:373:30: note: 'prev_seg' was declared here 373 | seg_element *first_seg, *prev_seg; | ^~~~~~~~ run_vegaMC.c:461:29: warning: 'first_seg' may be used uninitialized [-Wmaybe-uninitialized] 461 | for (i = 0; i < (tmp->num_regions); i++) { | ~~~~^~~~~~~~~~~~~~ run_vegaMC.c:373:18: note: 'first_seg' was declared here 373 | seg_element *first_seg, *prev_seg; | ^~~~~~~~~ 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 sort_data.c -o sort_data.o 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 vegaMC.c -o vegaMC.o vegaMC.c: In function 'heap_delete': vegaMC.c:235:10: warning: variable 'deleted' set but not used [-Wunused-but-set-variable] 235 | node deleted; | ^~~~~~~ vegaMC.c: In function 'init_trivial_segmentation': vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable] 592 | int i, j, index; | ^~~~~ gcc -shared -s -static-libgcc -o VegaMC.dll tmp.def run_vegaMC.o sort_data.o vegaMC.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-VegaMC/00new/VegaMC/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 (VegaMC)
VegaMC.Rcheck/VegaMC-Ex.timings
name | user | system | elapsed | |
VegaMC-package | 0.30 | 0.04 | 0.45 | |
sortData | 0.50 | 0.01 | 0.51 | |
vegaMC-methods | 0.30 | 0.03 | 0.38 | |