| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:32 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
To the developers/maintainers of the sSNAPPY package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sSNAPPY.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1992/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sSNAPPY 1.3.4 (landing page) Wenjun Liu
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: sSNAPPY |
| Version: 1.3.4 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:sSNAPPY.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings sSNAPPY_1.3.4.tar.gz |
| StartedAt: 2023-04-11 23:53:30 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-12 00:02:17 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 527.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sSNAPPY.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:sSNAPPY.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings sSNAPPY_1.3.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/sSNAPPY.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘sSNAPPY/DESCRIPTION’ ... OK
* this is package ‘sSNAPPY’ version ‘1.3.4’
* 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 ‘sSNAPPY’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 R 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 ... OK
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
rank_gene_pert 58.008 0.840 58.848
pathway_pert 43.264 1.808 45.074
raw_gene_pert 36.081 0.836 36.917
plot_gene_contribution 35.833 0.860 36.693
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘sSNAPPY.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/sSNAPPY.Rcheck/00check.log’
for details.
sSNAPPY.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL sSNAPPY
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘sSNAPPY’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c GenePertScore.cpp -o GenePertScore.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/armadillo:26,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from GenePertScore.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:338:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:343:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:346:61: note: ‘#pragma message: INFO: see the documentation for details’
346 | #pragma message ("INFO: see the documentation for details")
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c code.cpp -o code.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c normaliseByPermutation.cpp -o normaliseByPermutation.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/armadillo:26,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from normaliseByPermutation.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:338:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:343:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:346:61: note: ‘#pragma message: INFO: see the documentation for details’
346 | #pragma message ("INFO: see the documentation for details")
| ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o sSNAPPY.so GenePertScore.o RcppExports.o code.o normaliseByPermutation.o -fopenmp -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-sSNAPPY/00new/sSNAPPY/libs
** R
** data
** 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 (sSNAPPY)
sSNAPPY.Rcheck/tests/spelling.Rout
R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.167 0.017 0.173
sSNAPPY.Rcheck/tests/testthat.Rout
R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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(sSNAPPY)
>
> test_check("sSNAPPY")
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 115 ]
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 115 ]
>
> proc.time()
user system elapsed
35.663 2.329 35.577
sSNAPPY.Rcheck/sSNAPPY-Ex.timings
| name | user | system | elapsed | |
| generate_permuted_scores | 0.328 | 0.004 | 0.332 | |
| normalise_by_permu | 0.001 | 0.000 | 0.000 | |
| pathway_pert | 43.264 | 1.808 | 45.074 | |
| plot_community | 2.519 | 0.060 | 2.581 | |
| plot_gene_contribution | 35.833 | 0.860 | 36.693 | |
| plot_gs2gene | 4.572 | 0.052 | 4.625 | |
| plot_gs_network | 0.724 | 0.012 | 0.737 | |
| rank_gene_pert | 58.008 | 0.840 | 58.848 | |
| raw_gene_pert | 36.081 | 0.836 | 36.917 | |
| retrieve_topology | 0.889 | 0.000 | 0.890 | |
| weight_ss_fc | 0.281 | 0.000 | 0.282 | |