Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 2228/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VegaMC 3.45.0 (landing page) Sandro Morganella
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: VegaMC |
Version: 3.45.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:VegaMC.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings VegaMC_3.45.0.tar.gz |
StartedAt: 2024-12-24 12:29:16 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 12:32:09 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 173.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: VegaMC.Rcheck |
Warnings: 6 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:VegaMC.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings VegaMC_3.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/VegaMC.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘VegaMC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VegaMC’ version ‘3.45.0’ * 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:144:13: warning: too many arguments for format [-Wformat-extra-args] run_vegaMC.c:149:13: warning: too many arguments for format [-Wformat-extra-args] Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/VegaMC.Rcheck/00install.out’ for details. * used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * checking installed package size ... INFO 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 Namespace in Imports field not imported from: ‘methods’ All declared Imports should be used. * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 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 ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/VegaMC/libs/VegaMC.so’: Found ‘rand’, possibly from ‘rand’ (C) Found ‘sprintf’, possibly from ‘sprintf’ (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 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: 6 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/VegaMC.Rcheck/00check.log’ for details.
VegaMC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL VegaMC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘VegaMC’ ... ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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; | ^~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c sort_data.c -o sort_data.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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; | ^~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-VegaMC/00new/VegaMC/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (VegaMC)
VegaMC.Rcheck/VegaMC-Ex.timings
name | user | system | elapsed | |
VegaMC-package | 0.178 | 0.013 | 0.431 | |
sortData | 0.215 | 0.008 | 0.227 | |
vegaMC-methods | 0.161 | 0.008 | 0.172 | |