Leonardo Collado-Torres
| Snapshot Date: 2018-10-13 16:45:11 -0400 (Sat, 13 Oct 2018) |
| URL: https://git.bioconductor.org/packages/derfinder |
| Branch: RELEASE_3_7 |
| Last Commit: 7be868d |
| Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-14 10:47:49 -0400 (Sun, 14 Oct 2018).
| Package 370/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| derfinder 1.14.0 Leonardo Collado-Torres
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: derfinder |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:derfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings derfinder_1.14.0.tar.gz |
| StartedAt: 2018-10-14 01:40:06 -0400 (Sun, 14 Oct 2018) |
| EndedAt: 2018-10-14 01:53:18 -0400 (Sun, 14 Oct 2018) |
| EllapsedTime: 792.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: derfinder.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:derfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings derfinder_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/derfinder.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'derfinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'derfinder' version '1.14.0'
* 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 'derfinder' 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
Unexported objects imported by ':::' calls:
'GenomeInfoDb:::.guessSpeciesStyle'
'GenomeInfoDb:::.supportedSeqnameMappings'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.smootherFstats'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
coverageToExon 5.31 0.34 5.66
makeGenomicState 5.59 0.01 5.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R'
OK
** running tests for arch 'x64' ...
Running 'test-all.R'
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 NOTE
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/derfinder.Rcheck/00check.log'
for details.
derfinder.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/derfinder_1.14.0.tar.gz && rm -rf derfinder.buildbin-libdir && mkdir derfinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=derfinder.buildbin-libdir derfinder_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL derfinder_1.14.0.zip && rm derfinder_1.14.0.tar.gz derfinder_1.14.0.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 254k 100 254k 0 0 4779k 0 --:--:-- --:--:-- --:--:-- 5421k
install for i386
* installing *source* package 'derfinder' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
** help
*** installing help indices
converting help for package 'derfinder'
finding HTML links ... done
analyzeChr html
annotateRegions html
calculatePvalues html
calculateStats html
coerceGR html
collapseFullCoverage html
coverageToExon html
createBw html
createBwSample html
define_cluster html
derfinder-deprecated html
derfinder-package html
extendedMapSeqlevels html
filterData html
findRegions html
fullCoverage html
genomeData html
genomeDataRaw html
genomeFstats html
genomeInfo html
genomeRegions html
genomicState html
getRegionCoverage html
getTotalMapped html
loadCoverage html
makeGenomicState html
makeModels html
mergeResults html
preprocessCoverage html
railMatrix html
rawFiles html
regionMatrix html
sampleDepth html
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
In R CMD INSTALL
install for x64
* installing *source* package 'derfinder' ...
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
* MD5 sums
packaged installation of 'derfinder' as derfinder_1.14.0.zip
* DONE (derfinder)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'derfinder' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
derfinder.Rcheck/tests_i386/test-all.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE
>
> flag <- as.logical(Sys.getenv('R_DISABLE_TESTS'))
> if(is.na(flag) | flag == FALSE) {
+ library('testthat')
+ test_check('derfinder')
+ }
Loading required package: derfinder
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
== testthat results ===========================================================
OK: 115 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
188.45 6.51 194.96
|
derfinder.Rcheck/tests_x64/test-all.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE
>
> flag <- as.logical(Sys.getenv('R_DISABLE_TESTS'))
> if(is.na(flag) | flag == FALSE) {
+ library('testthat')
+ test_check('derfinder')
+ }
Loading required package: derfinder
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
bplogdir: NA
== testthat results ===========================================================
OK: 115 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
222.59 5.59 228.23
|
|
derfinder.Rcheck/examples_i386/derfinder-Ex.timings
|
derfinder.Rcheck/examples_x64/derfinder-Ex.timings
|