Crispin Miller
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/simpleaffy |
| Branch: RELEASE_3_6 |
| Last Commit: 6876e02 |
| Last Changed Date: 2017-10-30 12:38:58 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
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 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings simpleaffy_2.54.0.tar.gz
###
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* 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 | |