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This page was generated on 2023-04-12 11:05:34 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 genoCN on palomino4


To the developers/maintainers of the genoCN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genoCN.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 776/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoCN 1.50.0  (landing page)
Wei Sun
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/genoCN
git_branch: RELEASE_3_16
git_last_commit: e166b5b
git_last_commit_date: 2022-11-01 11:04:55 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: genoCN
Version: 1.50.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genoCN.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings genoCN_1.50.0.tar.gz
StartedAt: 2023-04-11 01:48:02 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 01:48:58 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 56.1 seconds
RetCode: 0
Status:   OK  
CheckDir: genoCN.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genoCN.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings genoCN_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/genoCN.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'genoCN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoCN' version '1.50.0'
* 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 'genoCN' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
genoCNA: no visible binding for global variable 'init.Para.CNA'
genoCNV: no visible binding for global variable 'init.Para.CNV'
Undefined global functions or variables:
  init.Para.CNA init.Para.CNV
* 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 x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/genoCN/libs/x64/genoCN.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 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
genoCNA 11.79   0.62   12.45
* 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-3.16-bioc/meat/genoCN.Rcheck/00check.log'
for details.



Installation output

genoCN.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL genoCN
###
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'genoCN' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c tnorm_mle.c -o tnorm_mle.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c utility.c -o utility.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c xCNV.c -o xCNV.o
xCNV.c: In function 'emiss':
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
  317 |   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
      |                         ^
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
  317 |   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
      |                ^
xCNV.c: In function 'baum_welch':
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
  787 |   double mu_b_tmp, sd_b_tmp;
      |                    ^~~~~~~~
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
  787 |   double mu_b_tmp, sd_b_tmp;
      |          ^~~~~~~~
xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable]
  762 |   int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
      |          ^~
xCNV.c:1839:17: warning: 'pbf' may be used uninitialized in this function [-Wmaybe-uninitialized]
 1839 |                 weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xCNV.c:1839:17: warning: 'nGtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-genoCN/00new/genoCN/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 (genoCN)

Tests output


Example timings

genoCN.Rcheck/genoCN-Ex.timings

nameusersystemelapsed
genoCNA11.79 0.6212.45
genoCNV3.00.33.3
init.Para.CNA000
init.Para.CNV000
plotCN1.040.051.10
snpData0.990.041.04
snpInfo1.010.071.08