Jitao David Zhang
| Snapshot Date: 2024-04-28 14:00:16 -0400 (Sun, 28 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/BioQC |
| git_branch: devel |
| git_last_commit: aab37ed |
| git_last_commit_date: 2023-10-24 10:46:32 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-04-29 11:40:35 -0400 (Mon, 29 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4752 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4475 |
| 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 217/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioQC 1.31.0 (landing page) Jitao David Zhang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the BioQC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioQC.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: BioQC |
| Version: 1.31.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:BioQC.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings BioQC_1.31.0.tar.gz |
| StartedAt: 2024-04-29 04:05:31 -0000 (Mon, 29 Apr 2024) |
| EndedAt: 2024-04-29 04:06:29 -0000 (Mon, 29 Apr 2024) |
| EllapsedTime: 58.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioQC.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:BioQC.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings BioQC_1.31.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BioQC.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioQC’ version ‘1.31.0’
* package encoding: UTF-8
* 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 ‘BioQC’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
extdata 3.9Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) readCurrentSignatures.Rd:13: Lost braces
13 | \item{namespace}{Character, namespace of the gene-set, or code{NULL}, passed
| ^
checkRd: (-1) wmwTest.Rd:282: Lost braces
282 | code{wilcox.test} in the \code{stats} package, and \code{rankSumTestWithCorrelation} in
| ^
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/BioQC.Rcheck/00check.log’
for details.
BioQC.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL BioQC
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘BioQC’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG `/home/biocbuild/R/R-beta-2024-04-15_r86425/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gini.c -o gini.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG `/home/biocbuild/R/R-beta-2024-04-15_r86425/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG `/home/biocbuild/R/R-beta-2024-04-15_r86425/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c read_gmt.cpp -o read_gmt.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG `/home/biocbuild/R/R-beta-2024-04-15_r86425/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c stat_rank.c -o stat_rank.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG `/home/biocbuild/R/R-beta-2024-04-15_r86425/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c wmw_test.c -o wmw_test.o
wmw_test.c: In function ‘wmw_test_list’:
wmw_test.c:118: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
118 | #pragma omp parallel for
|
wmw_test.c: In function ‘wmw_test’:
wmw_test.c:168: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
168 | #pragma omp parallel for
|
wmw_test.c: In function ‘signed_wmw_test_list’:
wmw_test.c:201: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
201 | #pragma omp parallel for
|
wmw_test.c: In function ‘signed_wmw_test’:
wmw_test.c:270: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
270 | #pragma omp parallel for
|
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o BioQC.so gini.o init.o read_gmt.o stat_rank.o wmw_test.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-BioQC/00new/BioQC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (BioQC)
BioQC.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(BioQC)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> test_check("BioQC")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 125 ]
>
> proc.time()
user system elapsed
8.526 0.187 8.722
BioQC.Rcheck/BioQC-Ex.timings
| name | user | system | elapsed | |
| GmtList | 0.003 | 0.000 | 0.003 | |
| IndexList | 0.004 | 0.000 | 0.004 | |
| SignedGenesets | 0.002 | 0.000 | 0.002 | |
| SignedIndexList | 0.003 | 0.000 | 0.003 | |
| absLog10p | 0 | 0 | 0 | |
| appendGmtList | 0.005 | 0.000 | 0.006 | |
| as.GmtList | 0.000 | 0.000 | 0.001 | |
| entropy | 0.001 | 0.000 | 0.002 | |
| entropyDiversity | 0.011 | 0.000 | 0.011 | |
| entropySpecificity | 0.007 | 0.000 | 0.007 | |
| filterPmat | 0.001 | 0.000 | 0.000 | |
| getLeadingEdgeIndexFromVector | 0.003 | 0.000 | 0.003 | |
| gini | 0 | 0 | 0 | |
| gmtlist2signedGenesets | 0.004 | 0.000 | 0.005 | |
| matchGenes | 0.097 | 0.000 | 0.097 | |
| offset-set | 0.001 | 0.000 | 0.001 | |
| offset | 0.001 | 0.000 | 0.001 | |
| prettySigNames | 0.054 | 0.000 | 0.055 | |
| readCurrentSignatures | 0.051 | 0.000 | 0.051 | |
| readGmt | 0.072 | 0.000 | 0.074 | |
| readSignedGmt | 0.006 | 0.002 | 0.008 | |
| sampleSpecialization | 0.007 | 0.000 | 0.008 | |
| setNamespace | 0.007 | 0.000 | 0.008 | |
| simplifyMatrix | 0.000 | 0.000 | 0.001 | |
| sub-.GmtList | 0.002 | 0.000 | 0.003 | |
| sub-sub-.GmtList | 0.001 | 0.000 | 0.001 | |
| uniqGenesetsByNamespace | 0.008 | 0.000 | 0.007 | |
| wmwLeadingEdge | 0.009 | 0.000 | 0.009 | |
| wmwTest | 0.252 | 0.004 | 0.258 | |
| wmwTestInR | 0.004 | 0.000 | 0.005 | |