Sean Davis
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ACME |
| Branch: master |
| Last Commit: 67dae98 |
| Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:53:32 -0400 (Tue, 09 Apr 2019).
| Package 14/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ACME 2.39.0 Sean Davis
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: ACME |
| Version: 2.39.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ACME.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ACME_2.39.0.tar.gz |
| StartedAt: 2019-04-08 23:43:22 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:44:49 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 86.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ACME.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ACME.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ACME_2.39.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ACME.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ACME/DESCRIPTION’ ... OK
* this is package ‘ACME’ version ‘2.39.0’
* 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 ‘ACME’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 30.8Mb
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
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
findClosestGene 3.797 0.216 6.348
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/ACME.Rcheck/00check.log’
for details.
ACME.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ACME
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ACME’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c windowChisq.c -o windowChisq.o
windowChisq.c:57:71: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
^
windowChisq.c:57:71: note: place parentheses around the '>' expression to silence this warning
while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
^
windowChisq.c:57:71: note: place parentheses around the & expression to evaluate it first
while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
^
windowChisq.c:62:70: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
^
windowChisq.c:62:70: note: place parentheses around the '<' expression to silence this warning
while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
^
windowChisq.c:62:70: note: place parentheses around the & expression to evaluate it first
while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
^
windowChisq.c:21:11: warning: unused variable 'xa' [-Wunused-variable]
double *xa,*xlocations,*xchivals;
^
windowChisq.c:86:20: warning: incompatible function pointer types initializing 'DL_FUNC' (aka 'void *(*)()') with an expression of type 'SEXP (*)(SEXP, SEXP, SEXP, SEXP, SEXP)' (aka 'struct SEXPREC *(*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)') [-Wincompatible-function-pointer-types]
{"windowChisq",&windowChisq,5},
^˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ACME.so windowChisq.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-ACME/00new/ACME/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ACME)
ACME.Rcheck/ACME-Ex.timings
| name | user | system | elapsed | |
| ACMECalcSet-class | 2.075 | 0.281 | 2.357 | |
| ACMESet-class | 0.650 | 0.059 | 0.784 | |
| aGFF-class | 0.508 | 0.035 | 0.542 | |
| aGFFCalc-class | 1.752 | 0.197 | 1.949 | |
| do.aGFF.calc | 1.718 | 0.235 | 1.953 | |
| example.agff | 0.549 | 0.047 | 0.595 | |
| findClosestGene | 3.797 | 0.216 | 6.348 | |
| findRegions | 3.324 | 0.356 | 3.683 | |
| generics | 0.547 | 0.044 | 0.592 | |
| getRefflat | 2.376 | 0.127 | 4.294 | |
| read.resultsGFF | 4.374 | 0.280 | 4.659 | |
| write.bedGraph | 2.730 | 0.153 | 2.894 | |
| write.sgr | 2.410 | 0.156 | 2.576 | |