Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:20 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for CSSP on palomino3


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.

raw results

Package 442/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSSP 1.34.0  (landing page)
Chandler Zuo
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/CSSP
git_branch: RELEASE_3_15
git_last_commit: 91c182b
git_last_commit_date: 2022-04-26 11:15:36 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CSSP
Version: 1.34.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CSSP.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CSSP_1.34.0.tar.gz
StartedAt: 2022-10-18 23:20:25 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 23:21:32 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 66.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CSSP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CSSP.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CSSP_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/CSSP.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.34.0'
* 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
* 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 ... NOTE
File 'CSSP/libs/x64/CSSP.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gridSample.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gridSample.o'

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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 16.02      1   17.02
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/CSSP.Rcheck/00check.log'
for details.



Installation output

CSSP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CSSP
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CSSP' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bincount.c -o bincount.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c binpower.c -o binpower.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gridLogMean.c -o gridLogMean.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gridMGC.c -o gridMGC.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gridMean.c -o gridMean.o
gridMean.c: In function 'gridMGCmean_c':
gridMean.c:10:63: warning: unused variable 'counter' [-Wunused-variable]
   10 |   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]
  177 |   R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[2],n=length(map),newG,counter;
      |                                                               ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gridMode.c -o gridMode.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gridNonpa.c -o gridNonpa.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gridSample.c -o gridSample.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c tag2bin.c -o tag2bin.o
gcc -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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CSSP/00new/CSSP/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CSSP)

Tests output

CSSP.Rcheck/tests/run_tests.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 56 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 56 ]
> 
> proc.time()
   user  system elapsed 
   2.79    0.50    3.34 

Example timings

CSSP.Rcheck/CSSP-Ex.timings

nameusersystemelapsed
CSSPFit-class000
bindcount0.110.000.11
bindcount.chr0.020.000.02
callpeak-methods0.000.020.02
createBinData0.310.030.34
cssp.fit-methods3.220.093.31
cssp.power-methods16.02 1.0017.02
cssp.sim-methods0.000.030.03
fit.freq-methods0.220.020.23
pBBT-methods0.000.010.02
peakcount0.070.040.11
peakcount.chr0.020.000.01
qBBT-methods0.030.000.03
readBinFile0.000.030.04
tag2bin0.020.010.03
tag2bin.chr000