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This page was generated on 2024-03-01 11:39:38 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1935/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signeR 2.5.0  (landing page)
Renan Valieris
Snapshot Date: 2024-02-28 14:00:14 -0500 (Wed, 28 Feb 2024)
git_url: https://git.bioconductor.org/packages/signeR
git_branch: devel
git_last_commit: 40d75ce
git_last_commit_date: 2023-10-24 10:52:34 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for signeR on merida1


To the developers/maintainers of the signeR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/signeR.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.

raw results


Summary

Package: signeR
Version: 2.5.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signeR_2.5.0.tar.gz
StartedAt: 2024-02-29 10:51:34 -0500 (Thu, 29 Feb 2024)
EndedAt: 2024-02-29 11:07:07 -0500 (Thu, 29 Feb 2024)
EllapsedTime: 932.8 seconds
RetCode: 0
Status:   OK  
CheckDir: signeR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signeR_2.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/signeR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘signeR’ version ‘2.5.0’
* 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 ‘signeR’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 whether startup messages can be suppressed ... 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 ... NOTE
covariate: no visible binding for global variable ‘.’
explorepage: no visible binding for global variable ‘.’
genCountMatrixFromMAF: no visible binding for global variable
  ‘Variant_Type’
genCountMatrixFromMAF: no visible binding for global variable
  ‘Reference_Allele’
genCountMatrixFromMAF: no visible binding for global variable
  ‘Tumor_Seq_Allele2’
genCountMatrixFromMAF: no visible binding for global variable
  ‘Tumor_Seq_Allele1’
genCountMatrixFromVcf: no visible global function definition for
  ‘alt<-’
signeRFlow : server : loadSig: no visible binding for global variable
  ‘sig’
signeRFlow : server : loadSig: no visible binding for global variable
  ‘sig_test’
tcgaexplorer : get_similarities_tcga: no visible binding for global
  variable ‘project’
tcgaexplorer: no visible binding for global variable ‘.’
DiffExp,SignExp-character: no visible binding for global variable ‘fc’
ExposureBarplot,SignExp: no visible binding for global variable
  ‘Samples’
ExposureBarplot,SignExp: no visible binding for global variable
  ‘Signatures’
ExposureBoxplot,SignExp: no visible binding for global variable
  ‘Signatures’
ExposureBoxplot,SignExp: no visible binding for global variable
  ‘Samples’
ExposureClassify,ANY-character: no visible binding for global variable
  ‘Col’
ExposureClassify,ANY-character: no visible binding for global variable
  ‘Frequency’
ExposureClassify,ANY-character: no visible binding for global variable
  ‘Row’
ExposureClassifyCV,ANY-character: no visible binding for global
  variable ‘Col’
ExposureClassifyCV,ANY-character: no visible binding for global
  variable ‘Frequency’
ExposureClassifyCV,ANY-character: no visible binding for global
  variable ‘Row’
ExposureCorrelation,SignExp-numeric: no visible binding for global
  variable ‘Feature’
ExposureCorrelation,SignExp-numeric: no visible binding for global
  variable ‘exposure’
ExposureCorrelation,matrix-numeric: no visible binding for global
  variable ‘Feature’
ExposureCorrelation,matrix-numeric: no visible binding for global
  variable ‘exposure’
Undefined global functions or variables:
  . Col Feature Frequency Reference_Allele Row Samples Signatures
  Tumor_Seq_Allele1 Tumor_Seq_Allele2 Variant_Type alt<- exposure fc
  project sig sig_test
* checking Rd files ... NOTE
prepare_Rd: cosmic_data.Rd:91-93: Dropping empty section \details
prepare_Rd: cosmic_data.Rd:98-100: Dropping empty section \references
prepare_Rd: cosmic_data.Rd:101-102: Dropping empty section \examples
prepare_Rd: tcga_similarities.Rd:96-98: Dropping empty section \details
prepare_Rd: tcga_similarities.Rd:99-101: Dropping empty section \source
prepare_Rd: tcga_similarities.Rd:102-104: Dropping empty section \references
prepare_Rd: tcga_similarities.Rd:105-106: Dropping empty section \examples
prepare_Rd: tcga_tumors.Rd:18-20: Dropping empty section \details
prepare_Rd: tcga_tumors.Rd:21-23: Dropping empty section \source
prepare_Rd: tcga_tumors.Rd:24-26: Dropping empty section \references
prepare_Rd: tcga_tumors.Rd:27-28: Dropping empty section \examples
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... 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
ExposureFuzzyClustering 12.813  0.394  15.980
ExposureClassifyCV      12.266  0.160  14.771
ExposureClassify         8.155  0.105   9.873
ExposureSurvModel        7.356  0.174   8.999
Diffexp                  6.268  0.198   7.781
genMatrix                5.411  0.247   6.779
methods                  5.034  0.055   6.078
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/signeR.Rcheck/00check.log’
for details.



Installation output

signeR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL signeR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘signeR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fuzzy.cpp -o fuzzy.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gibbs_2.cpp -o gibbs_2.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c signeR_init.c -o signeR_init.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o signeR.so RcppExports.o fuzzy.o gibbs_2.o signeR_init.o -Wl,-S -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -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-signeR/00new/signeR/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (signeR)

Tests output


Example timings

signeR.Rcheck/signeR-Ex.timings

nameusersystemelapsed
Diffexp6.2680.1987.781
ExposureClassify8.1550.1059.873
ExposureClassifyCV12.266 0.16014.771
ExposureCorrelation3.4560.0454.259
ExposureFuzzyClustering12.813 0.39415.980
ExposureGLM2.5920.0343.215
ExposureHierarchicalClustering2.2550.0662.840
ExposureSurvModel7.3560.1748.999
ExposureSurvival3.1660.0413.852
genMatrix5.4110.2476.779
methods5.0340.0556.078
plots3.670.054.66
signeR-package0.0020.0010.004
signeR0.0030.0010.005