Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:07:03 -0400 (Thu, 12 Apr 2018).
Package 1302/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
simpleaffy 2.54.0 Crispin Miller
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | ![]() |
Package: simpleaffy |
Version: 2.54.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings simpleaffy_2.54.0.tar.gz |
StartedAt: 2018-04-12 02:58:40 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 03:00:48 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 127.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: simpleaffy.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings simpleaffy_2.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/simpleaffy.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘simpleaffy/DESCRIPTION’ ... OK * this is package ‘simpleaffy’ version ‘2.54.0’ * 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 ‘simpleaffy’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ ‘utils’ ‘grDevices’ ‘graphics’ ‘stats’ ‘BiocGenerics’ ‘Biobase’ ‘affy’ ‘genefilter’ ‘gcrma’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE hmap.eset : <anonymous>: no visible global function definition for ‘var’ hmap.pc : <anonymous>: no visible global function definition for ‘var’ qc.affy: no visible binding for global variable ‘var’ standard.pearson: no visible global function definition for ‘cor’ Undefined global functions or variables: cor var Consider adding importFrom("stats", "cor", "var") 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 methods: generic '[' and siglist 'PairComp,ANY,ANY,ANY' generic '[<-' and siglist 'PairComp,ANY,ANY,ANY' 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 File ‘simpleaffy/libs/simpleaffy.so’: Found ‘stderr’, possibly from ‘stderr’ (C) Object: ‘simpleaffy.o’ 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. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking installed files from ‘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 ‘/home/biocbuild/bbs-3.6-bioc/meat/simpleaffy.Rcheck/00check.log’ for details.
simpleaffy.Rcheck/00install.out
* installing *source* package ‘simpleaffy’ ... ** libs gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c simpleaffy.c -o simpleaffy.o simpleaffy.c: In function ‘bgmas’: simpleaffy.c:440:30: warning: passing argument 1 of ‘REprintf’ from incompatible pointer type [-Wincompatible-pointer-types] if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]); ^ In file included from /home/biocbuild/bbs-3.6-bioc/R/include/R.h:88:0, from simpleaffy.c:5: /home/biocbuild/bbs-3.6-bioc/R/include/R_ext/Print.h:43:6: note: expected ‘const char *’ but argument is of type ‘struct _IO_FILE *’ void REprintf(const char *, ...); ^ g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o simpleaffy.so simpleaffy.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.6-bioc/meat/simpleaffy.Rcheck/simpleaffy/libs ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (simpleaffy)
simpleaffy.Rcheck/simpleaffy-Ex.timings
name | user | system | elapsed | |
all.present | 0.000 | 0.000 | 0.001 | |
all.present.in.group | 0.000 | 0.000 | 0.001 | |
bg.correct.sa | 0 | 0 | 0 | |
call.exprs | 0 | 0 | 0 | |
detection.p.val | 0.000 | 0.000 | 0.001 | |
get.annotation | 0.000 | 0.000 | 0.001 | |
get.array.indices | 0.004 | 0.000 | 0.001 | |
get.array.subset | 0.000 | 0.000 | 0.001 | |
get.array.subset.affy | 0 | 0 | 0 | |
get.fold.change.and.t.test | 0 | 0 | 0 | |
hmap.colors | 0 | 0 | 0 | |
hmap.eset | 0 | 0 | 0 | |
hmap.pc | 0.000 | 0.000 | 0.001 | |
journalpng | 0.004 | 0.000 | 0.001 | |
justMAS | 0 | 0 | 0 | |
pairwise.comparison | 0 | 0 | 0 | |
pairwise.filter | 0 | 0 | 0 | |
plot.pairwise.comparison | 0.000 | 0.000 | 0.001 | |
plot.qc.stats | 0.052 | 0.004 | 0.057 | |
qc | 0.120 | 0.016 | 0.133 | |
qc.affy | 0.024 | 0.000 | 0.025 | |
qc.get.alpha1 | 0.012 | 0.000 | 0.012 | |
qc.get.array | 0.000 | 0.000 | 0.001 | |
qc.get.probes | 0.000 | 0.000 | 0.003 | |
qc.get.ratios | 0.000 | 0.000 | 0.002 | |
qc.get.spikes | 0.000 | 0.000 | 0.001 | |
qc.have.params | 0.004 | 0.000 | 0.004 | |
qc.ok | 0.000 | 0.000 | 0.002 | |
qc.read.file | 0.000 | 0.000 | 0.002 | |
qc.stats | 0.020 | 0.000 | 0.018 | |
read.affy | 0.000 | 0.000 | 0.001 | |
read.affy.mixed | 0 | 0 | 0 | |
setQCEnvironment | 0.020 | 0.000 | 0.019 | |
simpleaffy-deprecated | 0.008 | 0.000 | 0.008 | |
standard.pearson | 0.000 | 0.000 | 0.001 | |
trad.scatter.plot | 0.004 | 0.000 | 0.000 | |