Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2244/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VegaMC 3.44.0 (landing page) Sandro Morganella
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 3.44.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VegaMC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VegaMC_3.44.0.tar.gz |
StartedAt: 2024-12-20 11:14:53 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 11:18:33 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 219.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: VegaMC.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VegaMC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VegaMC_3.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/VegaMC.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘VegaMC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VegaMC’ version ‘3.44.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘VegaMC’ can be installed ... WARNING Found the following significant warnings: run_vegaMC.c:144:62: warning: data argument not used by format string [-Wformat-extra-args] run_vegaMC.c:150:13: warning: data argument not used by format string [-Wformat-extra-args] run_vegaMC.c:491:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] run_vegaMC.c:526:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] sort_data.c:131:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] sort_data.c:180:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] vegaMC.c:458:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/VegaMC.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.4Mb 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 ... WARNING Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/VegaMC/libs/VegaMC.so’: Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C) 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: 2 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/VegaMC.Rcheck/00check.log’ for details.
VegaMC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VegaMC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘VegaMC’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c run_vegaMC.c -o run_vegaMC.o run_vegaMC.c:144:62: warning: data argument not used by format string [-Wformat-extra-args] Rprintf("\tAberration Matrices Successfully Computed\n", num_seg_regions); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ run_vegaMC.c:150:13: warning: data argument not used by format string [-Wformat-extra-args] num_seg_regions); ^ run_vegaMC.c:491:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] elem = strtok('\0', sep); ^~~~ run_vegaMC.c:526:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] elem = strtok('\0', sep); ^~~~ run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable] char *elem, *brkt; ^ 5 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sort_data.c -o sort_data.o sort_data.c:131:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] elem = strtok('\0', sep); ^~~~ sort_data.c:180:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] elem = strtok('\0', sep); ^~~~ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vegaMC.c -o vegaMC.o vegaMC.c:235:10: warning: variable 'deleted' set but not used [-Wunused-but-set-variable] node deleted; ^ vegaMC.c:458:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] lambda_gradient = abs(lambda); ^ vegaMC.c:458:23: note: use function 'fabsf' instead lambda_gradient = abs(lambda); ^~~ fabsf vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable] int i, j, index; ^ 3 warnings generated. clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-VegaMC/00new/VegaMC/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** 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 | 0.195 | 0.070 | 0.268 | |
sortData | 0.382 | 0.069 | 0.460 | |
vegaMC-methods | 0.192 | 0.018 | 0.221 | |