Renee X. de Menezes
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SIM |
| Branch: RELEASE_3_8 |
| Last Commit: 0d16b7e |
| Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:20:44 -0400 (Sat, 13 Apr 2019).
| Package 1448/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SIM 1.52.0 Renee X. de Menezes
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SIM |
| Version: 1.52.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SIM_1.52.0.tar.gz |
| StartedAt: 2019-04-13 05:33:05 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:36:46 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 220.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIM.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SIM_1.52.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SIM.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SIM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIM' version '1.52.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'SIM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
'library' or 'require' call to 'biomaRt' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'quantreg'
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 'SIM/R/zzz.R':
.onAttach calls:
library.dynam("SIM", pkg, lib)
See section 'Good practice' in '?.onAttach'.
dependent.heatmap: warning in get(as.character(adjust[[2]]), env =
attr(adjust, ".Environment")): partial argument match of 'env' to
'envir'
sim.plot.zoom.in: warning in eval(call, env = attr(call, "env")):
partial argument match of 'env' to 'envir'
sim.update.chrom.table: warning in factor(table$name, level = c(1:22,
"X", "Y")): partial argument match of 'level' to 'levels'
assemble.data: no visible global function definition for 'data'
assemble.data: no visible binding for global variable 'chrom.table'
convertGenomicRegion: no visible global function definition for 'data'
convertGenomicRegion: no visible binding for global variable
'chrom.table'
dependent.heatmap: no visible global function definition for 'strwidth'
getoverlappingregions: no visible global function definition for
'useMart'
getoverlappingregions: no visible global function definition for
'getBM'
impute.nas.by.surrounding: no visible binding for global variable
'median'
impute.nas.by.surrounding: no visible global function definition for
'na.omit'
independent.heatmap: no visible global function definition for
'strwidth'
link.metadata: no visible binding for global variable 'expr.data'
link.metadata: no visible binding for global variable 'hgu133plus2CHR'
link.metadata: no visible binding for global variable
'hgu133plus2CHRLOC'
link.metadata: no visible binding for global variable
'hgu133plus2SYMBOL'
link.metadata: no visible global function definition for 'aggregate'
plotCytobands: no visible global function definition for 'data'
plotCytobands: no visible binding for global variable 'chrom.table'
quantsmooth.plot: no visible global function definition for 'rainbow'
showProgress: no visible global function definition for 'flush.console'
sim.plot.overlapping.indep.dep.features: no visible global function
definition for 'box'
sim.plot.pvals.on.genome: no visible global function definition for
'data'
sim.plot.pvals.on.genome: no visible binding for global variable
'chrom.table'
sim.plot.zoom.in: no visible global function definition for
'flush.console'
sim.plot.zoom.in: no visible global function definition for 'dev.new'
sim.plot.zscore.heatmap: no visible global function definition for
'colorRampPalette'
sim.update.chrom.table: no visible global function definition for
'dbConnect'
sim.update.chrom.table: no visible global function definition for
'MySQL'
sim.update.chrom.table: no visible global function definition for
'dbGetQuery'
tabulate.top.dep.features: no visible global function definition for
'na.omit'
tabulate.top.dep.features: no visible global function definition for
'write.table'
tabulate.top.indep.features: no visible global function definition for
'na.omit'
tabulate.top.indep.features: no visible global function definition for
'write.table'
validColumn: no visible global function definition for 'type.convert'
Undefined global functions or variables:
MySQL aggregate box chrom.table colorRampPalette data dbConnect
dbGetQuery dev.new expr.data flush.console getBM hgu133plus2CHR
hgu133plus2CHRLOC hgu133plus2SYMBOL median na.omit rainbow strwidth
type.convert useMart write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.new", "rainbow")
importFrom("graphics", "box", "strwidth")
importFrom("stats", "aggregate", "median", "na.omit")
importFrom("utils", "data", "flush.console", "type.convert",
"write.table")
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 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-3.8-bioc/R/library/SIM/libs/i386/SIM.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
Examples with CPU or elapsed time > 5s
user system elapsed
SIM-package 6.91 0.07 6.97
integrated.analysis 5.78 0.00 5.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SIM-package 7.18 0.12 7.32
integrated.analysis 5.88 0.00 5.88
* 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/SIM.Rcheck/00check.log'
for details.
SIM.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/SIM_1.52.0.tar.gz && rm -rf SIM.buildbin-libdir && mkdir SIM.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIM.buildbin-libdir SIM_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SIM_1.52.0.zip && rm SIM_1.52.0.tar.gz SIM_1.52.0.zip
###
##############################################################################
##############################################################################
% 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 269k 100 269k 0 0 7234k 0 --:--:-- --:--:-- --:--:-- 7918k
install for i386
* installing *source* package 'SIM' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c withinWindow.c -o withinWindow.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o SIM.dll tmp.def withinWindow.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/SIM.buildbin-libdir/SIM/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SIM'
finding HTML links ... done
RESOURCERER.annotation.to.ID html
SIM-package html
acgh.data html
assemble.data html
chrom.table html
expr.data html
getoverlappingregions html
impute.nas.by.surrounding html
integrated.analysis html
link.metadata html
samples html
sim.plot.overlapping.indep.dep.features
html
sim.plot.pvals.on.genome html
sim.plot.pvals.on.region html
sim.plot.zoom.in html
sim.plot.zscore.heatmap html
sim.update.chrom.table html
tabulate.pvals html
tabulate.top.dep.features html
tabulate.top.indep.features html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'SIM' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c withinWindow.c -o withinWindow.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o SIM.dll tmp.def withinWindow.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/SIM.buildbin-libdir/SIM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIM' as SIM_1.52.0.zip
* DONE (SIM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SIM' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
SIM.Rcheck/examples_i386/SIM-Ex.timings
|
SIM.Rcheck/examples_x64/SIM-Ex.timings
|