BioC 3.4: CHECK report for ACME on tokay1
This page was generated on 2017-04-15 16:15:11 -0400 (Sat, 15 Apr 2017).
ACME 2.30.0
Sean Davis
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ACME | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
Summary
| Package: ACME
|
| Version: 2.30.0
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| Command: rm -rf ACME.buildbin-libdir ACME.Rcheck && mkdir ACME.buildbin-libdir ACME.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ACME.buildbin-libdir ACME_2.30.0.tar.gz >ACME.Rcheck\00install.out 2>&1 && cp ACME.Rcheck\00install.out ACME-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ACME.buildbin-libdir --install="check:ACME-install.out" --force-multiarch --no-vignettes --timings ACME_2.30.0.tar.gz
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| StartedAt: 2017-04-14 20:52:03 -0400 (Fri, 14 Apr 2017)
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| EndedAt: 2017-04-14 20:54:46 -0400 (Fri, 14 Apr 2017)
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| EllapsedTime: 162.6 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: ACME.Rcheck
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| Warnings: 0
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Command output
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### Running command:
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### rm -rf ACME.buildbin-libdir ACME.Rcheck && mkdir ACME.buildbin-libdir ACME.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ACME.buildbin-libdir ACME_2.30.0.tar.gz >ACME.Rcheck\00install.out 2>&1 && cp ACME.Rcheck\00install.out ACME-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ACME.buildbin-libdir --install="check:ACME-install.out" --force-multiarch --no-vignettes --timings ACME_2.30.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/ACME.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ACME/DESCRIPTION' ... OK
* this is package 'ACME' version '2.30.0'
* 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 'ACME' can be installed ... OK
* checking installed package size ... NOTE
installed size is 30.9Mb
sub-directories of 1Mb or more:
data 3.1Mb
extdata 27.3Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotACMECalcSet: no visible global function definition for 'par'
.plotACMECalcSet: no visible global function definition for 'axis'
.plotACMECalcSet: no visible global function definition for 'abline'
.plotACMESet: no visible global function definition for 'par'
do.aGFF.calc: no visible global function definition for 'quantile'
findClosestGene: no visible binding for global variable 'refflat'
findClosestGene: no visible binding for '<<-' assignment to 'refflat'
findRegions : <anonymous>: no visible global function definition for
'median'
getRefflat: no visible global function definition for 'download.file'
getRefflat: no visible global function definition for 'read.delim'
plotgff: no visible global function definition for 'par'
plotgffcalc: no visible global function definition for 'par'
plotgffcalc: no visible global function definition for 'axis'
plotgffcalc: no visible global function definition for 'abline'
read.resultsGFF: no visible global function definition for 'read.delim'
windowChisq: no visible global function definition for 'pchisq'
write.bedGraph: no visible global function definition for 'write.table'
write.sgr: no visible global function definition for 'write.table'
plot,ACMECalcSet: no visible global function definition for 'par'
plot,ACMECalcSet: no visible global function definition for 'axis'
plot,ACMECalcSet: no visible global function definition for 'abline'
plot,ACMESet: no visible global function definition for 'par'
plot,aGFF: no visible global function definition for 'par'
plot,aGFFCalc: no visible global function definition for 'par'
plot,aGFFCalc: no visible global function definition for 'axis'
plot,aGFFCalc: no visible global function definition for 'abline'
Undefined global functions or variables:
abline axis download.file median par pchisq quantile read.delim
refflat write.table
Consider adding
importFrom("graphics", "abline", "axis", "par")
importFrom("stats", "median", "pchisq", "quantile")
importFrom("utils", "download.file", "read.delim", "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-3.4-bioc/meat/ACME.buildbin-libdir/ACME/libs/i386/ACME.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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
read.resultsGFF 5.61 0.06 5.67
** 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/ACME.Rcheck/00check.log'
for details.
ACME.Rcheck/00install.out:
install for i386
* installing *source* package 'ACME' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c windowChisq.c -o windowChisq.o
windowChisq.c: In function 'windowChisq':
windowChisq.c:58:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
firstprobe>0) {
^
windowChisq.c:63:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
lastprobe<(na-1)) {
^
windowChisq.c:21:11: warning: unused variable 'xa' [-Wunused-variable]
double *xa,*xlocations,*xchivals;
^
windowChisq.c: At top level:
windowChisq.c:86:5: warning: initialization from incompatible pointer type
{"windowChisq",&windowChisq,5},
^
windowChisq.c:86:5: warning: (near initialization for 'callMethods[0].fun')
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o ACME.dll tmp.def windowChisq.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/ACME.buildbin-libdir/ACME/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'ACME' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c windowChisq.c -o windowChisq.o
windowChisq.c: In function 'windowChisq':
windowChisq.c:58:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
firstprobe>0) {
^
windowChisq.c:63:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
lastprobe<(na-1)) {
^
windowChisq.c:21:11: warning: unused variable 'xa' [-Wunused-variable]
double *xa,*xlocations,*xchivals;
^
windowChisq.c: At top level:
windowChisq.c:86:5: warning: initialization from incompatible pointer type
{"windowChisq",&windowChisq,5},
^
windowChisq.c:86:5: warning: (near initialization for 'callMethods[0].fun')
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o ACME.dll tmp.def windowChisq.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/ACME.buildbin-libdir/ACME/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ACME' as ACME_2.30.0.zip
* DONE (ACME)
ACME.Rcheck/examples_i386/ACME-Ex.timings:
| name | user | system | elapsed
|
| ACMECalcSet-class | 2.40 | 0.21 | 2.61 |
|
| ACMESet-class | 0.83 | 0.00 | 0.83 |
|
| aGFF-class | 0.73 | 0.01 | 0.75 |
|
| aGFFCalc-class | 2.53 | 0.11 | 2.64 |
|
| do.aGFF.calc | 2.49 | 0.09 | 2.58 |
|
| example.agff | 0.56 | 0.02 | 0.57 |
|
| findClosestGene | 3.17 | 0.09 | 4.16 |
|
| findRegions | 3.58 | 0.19 | 3.77 |
|
| generics | 0.75 | 0.03 | 0.78 |
|
| getRefflat | 2.42 | 0.06 | 3.44 |
|
| read.resultsGFF | 5.61 | 0.06 | 5.67 |
|
| write.bedGraph | 3.28 | 0.07 | 3.34 |
|
| write.sgr | 2.57 | 0.09 | 2.69 |
|
ACME.Rcheck/examples_x64/ACME-Ex.timings:
| name | user | system | elapsed
|
| ACMECalcSet-class | 2.20 | 0.19 | 2.39 |
|
| ACMESet-class | 0.5 | 0.0 | 0.5 |
|
| aGFF-class | 0.49 | 0.00 | 0.48 |
|
| aGFFCalc-class | 1.72 | 0.14 | 1.86 |
|
| do.aGFF.calc | 1.92 | 0.05 | 1.97 |
|
| example.agff | 0.54 | 0.01 | 0.57 |
|
| findClosestGene | 2.21 | 0.06 | 3.18 |
|
| findRegions | 3.22 | 0.25 | 3.47 |
|
| generics | 0.48 | 0.00 | 0.49 |
|
| getRefflat | 2.19 | 0.04 | 3.12 |
|
| read.resultsGFF | 4.94 | 0.04 | 4.99 |
|
| write.bedGraph | 2.92 | 0.02 | 2.93 |
|
| write.sgr | 2.44 | 0.04 | 2.49 |
|