Chandler Zuo
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/CSSP |
| git_branch: RELEASE_3_14 |
| git_last_commit: 0f0928b |
| git_last_commit_date: 2021-10-26 12:09:00 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:51 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the CSSP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CSSP.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 424/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CSSP 1.32.0 (landing page) Chandler Zuo
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CSSP |
| Version: 1.32.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CSSP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CSSP_1.32.0.tar.gz |
| StartedAt: 2022-04-12 12:06:02 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 12:07:17 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 74.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CSSP.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CSSP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CSSP_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CSSP.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CSSP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSSP’ version ‘1.32.0’
* 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 ‘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
* 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
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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cssp.power-methods 19.931 0.518 20.471
cssp.fit-methods 6.825 0.118 6.949
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.14-bioc/meat/CSSP.Rcheck/00check.log’
for details.
CSSP.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CSSP
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CSSP’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c bincount.c -o bincount.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c binpower.c -o binpower.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gridLogMean.c -o gridLogMean.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gridMGC.c -o gridMGC.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gridMean.c -o gridMean.o
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: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;
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gridMode.c -o gridMode.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gridNonpa.c -o gridNonpa.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gridSample.c -o gridSample.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c tag2bin.c -o tag2bin.o
clang -mmacosx-version-min=10.13 -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 CSSP.so bincount.o binpower.o gridLogMean.o gridMGC.o gridMean.o gridMode.o gridNonpa.o gridSample.o tag2bin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-CSSP/00new/CSSP/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 (CSSP)
CSSP.Rcheck/tests/run_tests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 [ FAIL 0 | WARN 6 | SKIP 0 | PASS 56 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 56 ] > > proc.time() user system elapsed 4.298 0.308 4.628
CSSP.Rcheck/CSSP-Ex.timings
| name | user | system | elapsed | |
| CSSPFit-class | 0.002 | 0.001 | 0.003 | |
| bindcount | 0.126 | 0.012 | 0.138 | |
| bindcount.chr | 0.018 | 0.003 | 0.021 | |
| callpeak-methods | 0.013 | 0.003 | 0.016 | |
| createBinData | 0.297 | 0.029 | 0.327 | |
| cssp.fit-methods | 6.825 | 0.118 | 6.949 | |
| cssp.power-methods | 19.931 | 0.518 | 20.471 | |
| cssp.sim-methods | 0.014 | 0.017 | 0.031 | |
| fit.freq-methods | 0.172 | 0.011 | 0.184 | |
| pBBT-methods | 0.008 | 0.001 | 0.010 | |
| peakcount | 0.118 | 0.012 | 0.131 | |
| peakcount.chr | 0.015 | 0.003 | 0.019 | |
| qBBT-methods | 0.030 | 0.002 | 0.031 | |
| readBinFile | 0.016 | 0.005 | 0.020 | |
| tag2bin | 0.016 | 0.013 | 0.029 | |
| tag2bin.chr | 0.007 | 0.004 | 0.010 | |