Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:07:50 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 CNORdt on machv2


To the developers/maintainers of the CNORdt package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNORdt.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 351/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORdt 1.36.0  (landing page)
A. MacNamara
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/CNORdt
git_branch: RELEASE_3_14
git_last_commit: 0a09111
git_last_commit_date: 2021-10-26 12:04:54 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CNORdt
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNORdt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNORdt_1.36.0.tar.gz
StartedAt: 2022-01-18 11:28:11 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 11:30:52 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 161.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CNORdt.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNORdt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNORdt_1.36.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CNORdt.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNORdt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORdt’ version ‘1.36.0’
* 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 ‘CNORdt’ 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
Package in Depends field not imported from: ‘abind’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gaBinaryDT: no visible global function definition for ‘runif’
getFitDT: no visible global function definition for ‘splinefun’
getFitDT: no visible global function definition for ‘optim’
shift: no visible global function definition for ‘tail’
shift: no visible global function definition for ‘head’
Undefined global functions or variables:
  head optim runif splinefun tail
Consider adding
  importFrom("stats", "optim", "runif", "splinefun")
  importFrom("utils", "head", "tail")
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 (user + system) or elapsed time > 5s
                      user system elapsed
cutAndPlotResultsDT 31.199  0.152  31.429
gaBinaryDT          30.241  0.068  30.361
* 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-3.14-bioc/meat/CNORdt.Rcheck/00check.log’
for details.



Installation output

CNORdt.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNORdt
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CNORdt’ ...
** 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 simulatorDT.c -o simulatorDT.o
simulatorDT.c:243:19: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
                        if((track_cond == nCond)) {
                            ~~~~~~~~~~~^~~~~~~~
simulatorDT.c:243:19: note: remove extraneous parentheses around the comparison to silence this warning
                        if((track_cond == nCond)) {
                           ~           ^       ~
simulatorDT.c:243:19: note: use '=' to turn this equality comparison into an assignment
                        if((track_cond == nCond)) {
                                       ^~
                                       =
simulatorDT.c:53:6: warning: unused variable 'nSignals' [-Wunused-variable]
        int nSignals = INTEGER(nSignals_in)[0];
            ^
simulatorDT.c:55:6: warning: unused variable 'nTimes' [-Wunused-variable]
        int nTimes = INTEGER(nTimes_in)[0];
            ^
3 warnings generated.
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 CNORdt.so simulatorDT.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-CNORdt/00new/CNORdt/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 (CNORdt)

Tests output


Example timings

CNORdt.Rcheck/CNORdt-Ex.timings

nameusersystemelapsed
computeScoreDT0.1380.0080.146
convert2array0.0140.0020.017
cutAndPlotResultsDT31.199 0.15231.429
gaBinaryDT30.241 0.06830.361
getFitDT0.0470.0020.049
simulatorDT0.0120.0020.013