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This page was generated on 2023-01-02 09:00:52 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for sSNAPPY on palomino5


To the developers/maintainers of the sSNAPPY package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1946/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sSNAPPY 1.3.2  (landing page)
Wenjun Liu
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/sSNAPPY
git_branch: master
git_last_commit: 401ea3f
git_last_commit_date: 2022-12-12 00:03:36 -0500 (Mon, 12 Dec 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: sSNAPPY
Version: 1.3.2
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sSNAPPY.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings sSNAPPY_1.3.2.tar.gz
StartedAt: 2022-12-29 03:56:29 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 04:04:34 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 485.0 seconds
RetCode: 0
Status:   OK  
CheckDir: sSNAPPY.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sSNAPPY.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings sSNAPPY_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/sSNAPPY.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sSNAPPY/DESCRIPTION' ... OK
* this is package 'sSNAPPY' version '1.3.2'
* 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 whether package 'sSNAPPY' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/sSNAPPY/libs/x64/sSNAPPY.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
rank_gene_pert         51.67   1.61   53.30
pathway_pert           33.70   1.34   35.07
plot_gene_contribution 30.25   1.41   31.67
raw_gene_pert          28.93   1.14   30.08
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/sSNAPPY.Rcheck/00check.log'
for details.

Installation output

sSNAPPY.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL sSNAPPY
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'sSNAPPY' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GenePertScore.cpp -o GenePertScore.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/armadillo:22,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:56,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from GenePertScore.cpp:2:
F:/biocbuild/bbs-3.17-bioc/R/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")
      |                                                                                      ^
F:/biocbuild/bbs-3.17-bioc/R/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")
      |                                                                           ^
F:/biocbuild/bbs-3.17-bioc/R/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c code.cpp -o code.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c normaliseByPermutation.cpp -o normaliseByPermutation.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/armadillo:22,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:56,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from normaliseByPermutation.cpp:2:
F:/biocbuild/bbs-3.17-bioc/R/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")
      |                                                                                      ^
F:/biocbuild/bbs-3.17-bioc/R/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")
      |                                                                           ^
F:/biocbuild/bbs-3.17-bioc/R/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++ -shared -s -static-libgcc -o sSNAPPY.dll tmp.def GenePertScore.o RcppExports.o code.o normaliseByPermutation.o -fopenmp -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-sSNAPPY/00new/sSNAPPY/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sSNAPPY)

Tests output

sSNAPPY.Rcheck/tests/spelling.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   0.20    0.10    0.25

sSNAPPY.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 7 | SKIP 0 | PASS 115 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
  26.89    1.54  148.09

Example timings

sSNAPPY.Rcheck/sSNAPPY-Ex.timings

nameusersystemelapsed
generate_permuted_scores0.470.080.55
normalise_by_permu000
pathway_pert33.70 1.3435.07
plot_community2.220.222.47
plot_gene_contribution30.25 1.4131.67
plot_gs2gene3.440.123.56
plot_gs_network0.70.00.7
rank_gene_pert51.67 1.6153.30
raw_gene_pert28.93 1.1430.08
retrieve_topology0.710.020.75
weight_ss_fc0.490.060.55