Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:43 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the inveRsion package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/inveRsion.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 937/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
inveRsion 1.40.0 (landing page) Alejandro Caceres
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: inveRsion |
Version: 1.40.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:inveRsion.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings inveRsion_1.40.0.tar.gz |
StartedAt: 2021-10-14 10:17:10 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:18:18 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 68.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: inveRsion.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:inveRsion.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings inveRsion_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/inveRsion.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘inveRsion/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘inveRsion’ version ‘1.40.0’ * 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 ‘inveRsion’ can be installed ... WARNING Found the following significant warnings: inversionModel.c:185:31: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] inversionModel.c:360:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] See ‘/home/biocbuild/bbs-3.13-bioc/meat/inveRsion.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 ... NOTE Package in Depends field not imported from: ‘haplo.stats’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘inveRsion/R/zzz.R’: .onLoad calls: packageStartupMessage("\n") packageStartupMessage("Hola!\n") packageStartupMessage("welcome to inevRsion package. \n \n \n") packageStartupMessage("type: manual() for full manual \n vignette(\"inveRsion\") for a quick start \n") See section ‘Good practice’ in '?.onAttach'. callEncode: no visible global function definition for ‘quantile’ encodeGeno: no visible global function definition for ‘setupGeno’ encodeGeno: no visible global function definition for ‘haplo.em’ encodeGeno: no visible global function definition for ‘haplo.em.control’ encodeGenoAcross: no visible global function definition for ‘setupGeno’ encodeGenoAcross: no visible global function definition for ‘haplo.em’ encodeGenoAcross: no visible global function definition for ‘haplo.em.control’ Undefined global functions or variables: haplo.em haplo.em.control quantile setupGeno Consider adding importFrom("stats", "quantile") 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 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 * 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, 4 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/inveRsion.Rcheck/00check.log’ for details.
inveRsion.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL inveRsion ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘inveRsion’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init_inveRsion.c -o init_inveRsion.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c inversionModel.c -o inversionModel.o inversionModel.c: In function ‘blockAndLev’: inversionModel.c:185:31: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] 185 | if(dat[(*nr)*(c1)+row]==levelleft[level] & dat[(*nr)*(c2)+row]==levelright[level]) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ inversionModel.c: In function ‘inversionModel’: inversionModel.c:360:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] 360 | while(steps<*maxSteps & tol>mintol) | ~~~~~^~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c writeGenoDat.c -o writeGenoDat.o writeGenoDat.c: In function ‘writeGenoDat’: writeGenoDat.c:34:16: warning: ‘dat’ may be used uninitialized in this function [-Wmaybe-uninitialized] 34 | int i,j,l,k,dat,nomiss[*numlevcaco],sum[*numlevcaco]; | ^~~ gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o inveRsion.so init_inveRsion.o inversionModel.o writeGenoDat.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-inveRsion/00new/inveRsion/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 (inveRsion)
inveRsion.Rcheck/inveRsion-Ex.timings
name | user | system | elapsed | |
GenoDat-class | 0.001 | 0.004 | 0.006 | |
GenoDatROI-class | 0.010 | 0.000 | 0.011 | |
HaploCode-class | 0.059 | 0.004 | 0.063 | |
ac | 0.003 | 0.000 | 0.003 | |
accBic | 0.924 | 0.044 | 0.969 | |
accuracy-class | 0.017 | 0.003 | 0.021 | |
codeHaplo | 0.041 | 0.004 | 0.046 | |
gDat | 0.001 | 0.004 | 0.005 | |
getClassif-methods | 0.074 | 0.000 | 0.074 | |
getInv-methods | 0.002 | 0.000 | 0.001 | |
getROIs-methods | 0.002 | 0.000 | 0.002 | |
hapCode | 0.006 | 0.004 | 0.009 | |
invList | 0.000 | 0.002 | 0.003 | |
inveRsion-package | 0.000 | 0.000 | 0.001 | |
inversionList-class | 0.002 | 0.000 | 0.003 | |
listInv-methods | 0.411 | 0.003 | 0.413 | |
scan-class | 0.007 | 0.000 | 0.007 | |
scanInv | 0.034 | 0.007 | 0.042 | |
scanRes | 0.004 | 0.000 | 0.004 | |
setUpGenoDatFile | 0.006 | 0.001 | 0.008 | |