Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:08:30 -0400 (Wed, 15 Apr 2020).
Package 1515/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
sapFinder 1.24.0 Shaohang Xu
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | ERROR | ERROR | skipped | skipped |
Package: sapFinder |
Version: 1.24.0 |
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:sapFinder.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings sapFinder_1.24.0.tar.gz |
StartedAt: 2020-04-15 02:06:43 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 02:08:00 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 76.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sapFinder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:sapFinder.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings sapFinder_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/sapFinder.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sapFinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sapFinder’ version ‘1.24.0’ * 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 ‘sapFinder’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: extdata 2.0Mb libs 1.4Mb * 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 .spplot: no visible global function definition for ‘mtext’ .spplot: no visible global function definition for ‘axis’ .spplot: no visible global function definition for ‘points’ Sys.which2: no visible global function definition for ‘setNames’ Undefined global functions or variables: axis mtext points setNames Consider adding importFrom("graphics", "axis", "mtext", "points") importFrom("stats", "setNames") to your NAMESPACE file. * 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 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 compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed easyRun 16.228 1.800 11.746 reportCreator 14.268 1.844 12.269 parserGear 11.100 1.660 8.301 dbCreator 8.784 1.364 6.548 runTandem 7.352 1.468 6.828 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 4 NOTEs See ‘/home/biocbuild/bbs-3.10-bioc/meat/sapFinder.Rcheck/00check.log’ for details.
sapFinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL sapFinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘sapFinder’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c dataHandle.cpp -o dataHandle.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o sapFinder.so dataHandle.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-sapFinder/00new/sapFinder/libs ** R ** 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 (sapFinder)
sapFinder.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 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. > BiocGenerics:::testPackage("sapFinder") RUNIT TEST PROTOCOL -- Wed Apr 15 02:07:57 2020 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : sapFinder RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 0.832 0.040 0.871
sapFinder.Rcheck/sapFinder-Ex.timings
name | user | system | elapsed | |
dbCreator | 8.784 | 1.364 | 6.548 | |
easyRun | 16.228 | 1.800 | 11.746 | |
parserGear | 11.100 | 1.660 | 8.301 | |
reportCreator | 14.268 | 1.844 | 12.269 | |
runTandem | 7.352 | 1.468 | 6.828 | |