Crispin Miller
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/simpleaffy |
| Branch: RELEASE_3_11 |
| Last Commit: 0dfde26 |
| Last Changed Date: 2020-04-27 14:09:04 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:49 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE simpleaffy PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1668/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| simpleaffy 2.64.0 Crispin Miller
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: simpleaffy |
| Version: 2.64.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:simpleaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings simpleaffy_2.64.0.tar.gz |
| StartedAt: 2020-10-17 08:21:36 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 08:24:57 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 201.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: simpleaffy.Rcheck |
| Warnings: 3 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:simpleaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings simpleaffy_2.64.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/simpleaffy.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'simpleaffy/DESCRIPTION' ... OK
* this is package 'simpleaffy' version '2.64.0'
* 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 whether package 'simpleaffy' can be installed ... WARNING
Found the following significant warnings:
simpleaffy.c:440:30: warning: passing argument 1 of 'REprintf' from incompatible pointer type [-Wincompatible-pointer-types]
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/simpleaffy.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
all:
function(..., na.rm)
all.present:
function(x, calls, no)
all:
function(..., na.rm)
all.present.in.group:
function(x, group, members, calls, no)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Found the following apparent S3 methods exported but not registered:
all.present all.present.in.group plot.pairwise.comparison
plot.qc.stats
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* 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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/simpleaffy/libs/i386/simpleaffy.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/simpleaffy/libs/x64/simpleaffy.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/simpleaffy.Rcheck/00check.log'
for details.
simpleaffy.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/simpleaffy_2.64.0.tar.gz && rm -rf simpleaffy.buildbin-libdir && mkdir simpleaffy.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=simpleaffy.buildbin-libdir simpleaffy_2.64.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL simpleaffy_2.64.0.zip && rm simpleaffy_2.64.0.tar.gz simpleaffy_2.64.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 448k 100 448k 0 0 7034k 0 --:--:-- --:--:-- --:--:-- 7735k
install for i386
* installing *source* package 'simpleaffy' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:88,
from simpleaffy.c:5:
C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R_ext/Print.h:46:15: note: expected 'const char *' but argument is of type 'FILE *' {aka 'struct _iobuf *'}
void REprintf(const char *, ...);
^~~~~~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o simpleaffy.dll tmp.def simpleaffy.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/simpleaffy.buildbin-libdir/00LOCK-simpleaffy/00new/simpleaffy/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'simpleaffy'
finding HTML links ... done
PairComp-class html
QCStats-class html
all.present html
all.present.in.group html
bg.correct.sa html
call.exprs html
detection.p.val html
get.annotation html
get.array.indices html
get.array.subset html
get.array.subset.affy html
get.fold.change.and.t.test html
hmap.colors html
hmap.eset html
hmap.pc html
journalpng html
justMAS html
pairwise.comparison html
pairwise.filter html
plot.pairwise.comparison html
plot.qc.stats html
qc html
qc.affy html
qc.get.alpha1 html
qc.get.array html
qc.get.probes html
qc.get.ratios html
qc.get.spikes html
qc.have.params html
qc.ok html
qc.read.file html
qc.stats html
read.affy html
read.affy.mixed html
setQCEnvironment html
simpleaffy-deprecated html
standard.pearson html
trad.scatter.plot html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'simpleaffy' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:88,
from simpleaffy.c:5:
C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R_ext/Print.h:46:15: note: expected 'const char *' but argument is of type 'FILE *' {aka 'struct _iobuf *'}
void REprintf(const char *, ...);
^~~~~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o simpleaffy.dll tmp.def simpleaffy.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/simpleaffy.buildbin-libdir/simpleaffy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'simpleaffy' as simpleaffy_2.64.0.zip
* DONE (simpleaffy)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'simpleaffy' successfully unpacked and MD5 sums checked
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simpleaffy.Rcheck/examples_i386/simpleaffy-Ex.timings
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simpleaffy.Rcheck/examples_x64/simpleaffy-Ex.timings
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