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This page was generated on 2023-09-25 11:39:45 -0400 (Mon, 25 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4659
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4394
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4408
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4397
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

Package 14/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ADaCGH2 2.41.0  (landing page)
Ramon Diaz-Uriarte
Snapshot Date: 2023-09-24 14:05:06 -0400 (Sun, 24 Sep 2023)
git_url: https://git.bioconductor.org/packages/ADaCGH2
git_branch: devel
git_last_commit: e22bfef
git_last_commit_date: 2023-04-25 10:18:17 -0400 (Tue, 25 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for ADaCGH2 on kunpeng2


To the developers/maintainers of the ADaCGH2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ADaCGH2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ADaCGH2
Version: 2.41.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ADaCGH2.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings ADaCGH2_2.41.0.tar.gz
StartedAt: 2023-09-25 01:32:10 -0000 (Mon, 25 Sep 2023)
EndedAt: 2023-09-25 01:41:06 -0000 (Mon, 25 Sep 2023)
EllapsedTime: 535.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ADaCGH2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ADaCGH2.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings ADaCGH2_2.41.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ADaCGH2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘ADaCGH2/DESCRIPTION’ ... OK
* this is package ‘ADaCGH2’ version ‘2.41.0’
* 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 ‘ADaCGH2’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* 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 loading without being on the library search path ... 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
pSegment           44.871  5.461  44.199
pChromPlot         31.670 17.561  24.731
outputToCGHregions 31.413  2.752  20.110
inputToADaCGH       7.615  1.101   8.529
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ADaCGH2.Rnw’ using ‘latin1’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ADaCGH2.Rcheck/00check.log’
for details.



Installation output

ADaCGH2.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL ADaCGH2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘ADaCGH2’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:65:12: warning: unused variable ‘totalNorm’ [-Wunused-variable]
   65 |     double totalNorm;
      |            ^~~~~~~~~
r_haarseg.c: In function ‘ad_FindLocalPeaks’:
r_haarseg.c:152:8: warning: "/*" within comment [-Wcomment]
  152 |       }/* for j */
      |         
r_haarseg.c:176:8: warning: "/*" within comment [-Wcomment]
  176 |       }/* for j */
      |         
r_haarseg.c:128:9: warning: unused variable ‘j’ [-Wunused-variable]
  128 |   int k,j;
      |         ^
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:97:27: warning: ‘highNonNormed’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   97 |             highNonNormed += signal[highEnd]*weight[highEnd] - signal[k-1]*weight[k-1];
      |             ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:98:26: warning: ‘lowWeightSum’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   98 |             lowWeightSum += weight[k-1] - weight[lowEnd];
      |             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:99:27: warning: ‘highWeightSum’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   99 |             highWeightSum += weight[highEnd] - weight[k-1];
      |             ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:96:26: warning: ‘lowNonNormed’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   96 |             lowNonNormed += signal[lowEnd]*weight[lowEnd] - signal[k-1]*weight[k-1];
      |             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o ADaCGH2.so init.o r_haarseg.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-ADaCGH2/00new/ADaCGH2/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 (ADaCGH2)

Tests output


Example timings

ADaCGH2.Rcheck/ADaCGH2-Ex.timings

nameusersystemelapsed
cutFile0.0660.0362.100
inputToADaCGH7.6151.1018.529
outputToCGHregions31.413 2.75220.110
pChromPlot31.67017.56124.731
pSegment44.871 5.46144.199