Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:36:38 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the SamSPECTRAL package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1615/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SamSPECTRAL 1.44.0 (landing page) Habil
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: SamSPECTRAL |
Version: 1.44.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SamSPECTRAL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SamSPECTRAL_1.44.0.tar.gz |
StartedAt: 2021-05-06 05:49:04 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 05:49:35 -0400 (Thu, 06 May 2021) |
EllapsedTime: 31.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SamSPECTRAL.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SamSPECTRAL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SamSPECTRAL_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/SamSPECTRAL.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SamSPECTRAL/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SamSPECTRAL’ version ‘1.44.0’ * 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 ‘SamSPECTRAL’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 ... NOTE NB: .First.lib is obsolete and will not be used in R >= 3.0.0 .First.lib: no visible global function definition for ‘provide’ Civilized_Spectral_Clustering: no visible global function definition for ‘lm’ Civilized_Spectral_Clustering: no visible global function definition for ‘coef’ Civilized_Spectral_Clustering: no visible global function definition for ‘coefficients’ Civilized_Spectral_Clustering: no visible global function definition for ‘abline’ Civilized_Spectral_Clustering: no visible global function definition for ‘kmeans’ kneepointDetection: no visible global function definition for ‘lm’ kneepointDetection: no visible global function definition for ‘png’ kneepointDetection: no visible global function definition for ‘par’ kneepointDetection: no visible global function definition for ‘axis’ kneepointDetection: no visible global function definition for ‘title’ kneepointDetection: no visible global function definition for ‘abline’ kneepointDetection: no visible global function definition for ‘dev.off’ Undefined global functions or variables: abline axis coef coefficients dev.off kmeans lm par png provide title Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "abline", "axis", "par", "title") importFrom("stats", "coef", "coefficients", "kmeans", "lm") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 classes: ‘eigen’ All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.12-bioc/meat/SamSPECTRAL.Rcheck/00check.log’ for details.
SamSPECTRAL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SamSPECTRAL ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘SamSPECTRAL’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Rinit.c -o Rinit.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c conductance_computation.c -o conductance_computation.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c maximum_of_rows.c -o maximum_of_rows.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SamSPECTRAL.so Rinit.o conductance_computation.o maximum_of_rows.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-SamSPECTRAL/00new/SamSPECTRAL/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 (SamSPECTRAL)
SamSPECTRAL.Rcheck/SamSPECTRAL-Ex.timings
name | user | system | elapsed | |
Building_Communities | 0.000 | 0.001 | 0.001 | |
Civilized_Spectral_Clustering | 0.000 | 0.001 | 0.001 | |
Conductance_Calculation | 0.000 | 0.000 | 0.001 | |
Connecting | 0.000 | 0.001 | 0.001 | |
SamSPECTRAL-package | 0 | 0 | 0 | |
SamSPECTRAL | 0.000 | 0.000 | 0.001 | |
check.SamSPECTRAL.input | 0.001 | 0.001 | 0.000 | |
eigen.values.10 | 0.032 | 0.006 | 0.041 | |
eigen.values.1000 | 0.058 | 0.005 | 0.063 | |
kneepointDetection | 0.099 | 0.003 | 0.102 | |
small | 0.018 | 0.004 | 0.022 | |
stmFSC | 0.125 | 0.016 | 0.141 | |