Chandler Zuo
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/CSSP |
| Branch: RELEASE_3_6 |
| Last Commit: d0dcaef |
| Last Changed Date: 2017-10-30 12:40:04 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:23:03 -0400 (Thu, 12 Apr 2018).
| Package 315/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CSSP 1.16.0 Chandler Zuo
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: CSSP |
| Version: 1.16.0 |
| Command: rm -rf CSSP.buildbin-libdir CSSP.Rcheck && mkdir CSSP.buildbin-libdir CSSP.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CSSP.buildbin-libdir CSSP_1.16.0.tar.gz >CSSP.Rcheck\00install.out 2>&1 && cp CSSP.Rcheck\00install.out CSSP-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CSSP.buildbin-libdir --install="check:CSSP-install.out" --force-multiarch --no-vignettes --timings CSSP_1.16.0.tar.gz |
| StartedAt: 2018-04-11 23:18:33 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:20:22 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 108.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CSSP.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### rm -rf CSSP.buildbin-libdir CSSP.Rcheck && mkdir CSSP.buildbin-libdir CSSP.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CSSP.buildbin-libdir CSSP_1.16.0.tar.gz >CSSP.Rcheck\00install.out 2>&1 && cp CSSP.Rcheck\00install.out CSSP-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CSSP.buildbin-libdir --install="check:CSSP-install.out" --force-multiarch --no-vignettes --timings CSSP_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CSSP.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CSSP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CSSP' version '1.16.0'
* 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 'CSSP' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'methods' 'stats' 'utils'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.allFit: no visible global function definition for 'quantile'
.allFit: no visible global function definition for 'model.matrix'
.allFit: no visible global function definition for 'glm'
.csspfit : pval.nb.cont.trunc: no visible global function definition
for 'runif'
.csspfit : pval.nb.cont.trunc: no visible global function definition
for 'pnbinom'
.csspfit : pval.nb.cont: no visible global function definition for
'runif'
.csspfit : pval.nb.cont: no visible global function definition for
'pnbinom'
.csspfit : pval.mod.w: no visible global function definition for
'dnbinom'
.csspfit: no visible global function definition for 'pnbinom'
.csspfit: no visible global function definition for 'dnbinom'
.csspfit: no visible global function definition for 'weighted.mean'
.csspfit: no visible global function definition for 'na.omit'
.csspfit: no visible global function definition for 'new'
.gridFit: no visible global function definition for 'quantile'
.gridFit: no visible global function definition for 'model.matrix'
.gridFit: no visible global function definition for 'glm'
.gridFit: no visible global function definition for 'predict.glm'
.nonpaFit: no visible global function definition for 'quantile'
.nonpaFit: no visible global function definition for 'weighted.mean'
createBinData: no visible global function definition for 'read.table'
createBinData: no visible global function definition for 'new'
createBinData: no visible global function definition for 'na.omit'
readBinFile: no visible global function definition for 'read.table'
callpeak,CSSPFit: no visible global function definition for 'pnbinom'
callpeak,CSSPFit: no visible global function definition for 'pgamma'
cssp.power,CSSPFit: no visible global function definition for 'rgamma'
cssp.power,CSSPFit: no visible global function definition for 'rbinom'
cssp.power,CSSPFit: no visible global function definition for 'rpois'
cssp.power,CSSPFit: no visible global function definition for 'pnbinom'
cssp.power,CSSPFit: no visible global function definition for 'na.omit'
cssp.power,CSSPFit: no visible global function definition for 'pgamma'
cssp.power,CSSPFit: no visible global function definition for 'qnbinom'
cssp.power,CSSPFit: no visible global function definition for 'qgamma'
cssp.power,CSSPFit: no visible global function definition for 'runif'
cssp.power,CSSPFit: no visible global function definition for
'weighted.mean'
cssp.sim,CSSPFit: no visible global function definition for 'rgamma'
cssp.sim,CSSPFit: no visible global function definition for 'rbinom'
cssp.sim,CSSPFit: no visible global function definition for 'runif'
fit.freq,CSSPFit: no visible global function definition for 'quantile'
fit.freq,CSSPFit : <anonymous>: no visible global function definition
for 'dnbinom'
pBBT,CSSPFit: no visible global function definition for 'pgamma'
qBBT,CSSPFit: no visible global function definition for 'quantile'
qBBT,CSSPFit: no visible global function definition for 'uniroot'
show,CSSPFit: no visible global function definition for 'showClass'
Undefined global functions or variables:
dnbinom glm model.matrix na.omit new pgamma pnbinom predict.glm
qgamma qnbinom quantile rbinom read.table rgamma rpois runif
showClass uniroot weighted.mean
Consider adding
importFrom("methods", "new", "showClass")
importFrom("stats", "dnbinom", "glm", "model.matrix", "na.omit",
"pgamma", "pnbinom", "predict.glm", "qgamma", "qnbinom",
"quantile", "rbinom", "rgamma", "rpois", "runif", "uniroot",
"weighted.mean")
importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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-3.6-bioc/meat/CSSP.buildbin-libdir/CSSP/libs/i386/CSSP.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'rand', possibly from 'rand' (C)
Found 'srand', possibly from 'srand' (C)
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 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
cssp.power-methods 27.08 1.08 28.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cssp.power-methods 19.6 0.66 20.25
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_tests.R'
OK
** running tests for arch 'x64' ...
Running 'run_tests.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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/CSSP.Rcheck/00check.log'
for details.
CSSP.Rcheck/00install.out
install for i386
* installing *source* package 'CSSP' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c bincount.c -o bincount.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c binpower.c -o binpower.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c gridLogMean.c -o gridLogMean.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c gridMGC.c -o gridMGC.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c gridMean.c -o gridMean.o
gridMean.c: In function 'gridMGCmean_c':
gridMean.c:10:63: warning: unused variable 'counter' [-Wunused-variable]
R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[4],n=length(map),newG,counter;
^
gridMean.c: In function 'gridMmean_c':
gridMean.c:177:63: warning: unused variable 'counter' [-Wunused-variable]
R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[2],n=length(map),newG,counter;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c gridMode.c -o gridMode.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c gridNonpa.c -o gridNonpa.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c gridSample.c -o gridSample.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c tag2bin.c -o tag2bin.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CSSP.dll tmp.def bincount.o binpower.o gridLogMean.o gridMGC.o gridMean.o gridMode.o gridNonpa.o gridSample.o tag2bin.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/CSSP.buildbin-libdir/CSSP/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'CSSP'
finding HTML links ... done
BinData-class html
CSSPFit-class html
bin.data html
bindata.chr1 html
bindcount html
bindcount.chr html
bindpos html
callpeak-methods html
createBinData html
cssp.fit-methods html
cssp.power-methods html
cssp.sim-methods html
fit.freq-methods html
pBBT-methods html
peakcount html
peakcount.chr html
peakpos html
qBBT-methods html
readBinFile html
sampleFit html
tag2bin html
tag2bin.chr html
tagdat_chip html
tagdat_input html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'CSSP' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c bincount.c -o bincount.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c binpower.c -o binpower.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c gridLogMean.c -o gridLogMean.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c gridMGC.c -o gridMGC.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c gridMean.c -o gridMean.o
gridMean.c: In function 'gridMGCmean_c':
gridMean.c:10:63: warning: unused variable 'counter' [-Wunused-variable]
R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[4],n=length(map),newG,counter;
^
gridMean.c: In function 'gridMmean_c':
gridMean.c:177:63: warning: unused variable 'counter' [-Wunused-variable]
R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[2],n=length(map),newG,counter;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c gridMode.c -o gridMode.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c gridNonpa.c -o gridNonpa.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c gridSample.c -o gridSample.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c tag2bin.c -o tag2bin.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CSSP.dll tmp.def bincount.o binpower.o gridLogMean.o gridMGC.o gridMean.o gridMode.o gridNonpa.o gridSample.o tag2bin.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/CSSP.buildbin-libdir/CSSP/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CSSP' as CSSP_1.16.0.zip
* DONE (CSSP)
In R CMD INSTALL
In R CMD INSTALL
|
CSSP.Rcheck/tests_i386/run_tests.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" 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. > # -------------------------------------------------------------- > # © 2011 Winged Foot Capital Research, LLC - All rights reserved > # author: Suraj Gupta <suraj@wingedfootcapital.com> > # -------------------------------------------------------------- > > library( "testthat" ) > > # convert all warnings to errors > options( warn = 1 ) > > # run tests > # test_package( "CSSP" ) > test_check( "CSSP" ) Loading required package: CSSP == testthat results =========================================================== OK: 62 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 3.46 0.12 3.57 |
CSSP.Rcheck/tests_x64/run_tests.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" 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. > # -------------------------------------------------------------- > # © 2011 Winged Foot Capital Research, LLC - All rights reserved > # author: Suraj Gupta <suraj@wingedfootcapital.com> > # -------------------------------------------------------------- > > library( "testthat" ) > > # convert all warnings to errors > options( warn = 1 ) > > # run tests > # test_package( "CSSP" ) > test_check( "CSSP" ) Loading required package: CSSP == testthat results =========================================================== OK: 62 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 4.25 0.15 4.40 |
|
CSSP.Rcheck/examples_i386/CSSP-Ex.timings
|
CSSP.Rcheck/examples_x64/CSSP-Ex.timings
|