Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-20 11:35:59 -0400 (Mon, 20 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 322/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHcall 2.66.0  (landing page)
Mark van de Wiel
Snapshot Date: 2024-05-19 14:00:13 -0400 (Sun, 19 May 2024)
git_url: https://git.bioconductor.org/packages/CGHcall
git_branch: RELEASE_3_19
git_last_commit: 93313e9
git_last_commit_date: 2024-04-30 10:17:15 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for CGHcall on nebbiolo1


To the developers/maintainers of the CGHcall package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CGHcall.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.

raw results


Summary

Package: CGHcall
Version: 2.66.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CGHcall.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CGHcall_2.66.0.tar.gz
StartedAt: 2024-05-19 21:04:49 -0400 (Sun, 19 May 2024)
EndedAt: 2024-05-19 21:05:37 -0400 (Sun, 19 May 2024)
EllapsedTime: 47.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CGHcall.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CGHcall.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CGHcall_2.66.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CGHcall.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘CGHcall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CGHcall’ version ‘2.66.0’
* 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 ‘CGHcall’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Non-standard license specification:
  GPL (http://www.gnu.org/copyleft/gpl.html)
Standardizable: FALSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... WARNING
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘CGHcall’
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘snowfall’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘DNAcopy’ ‘methods’ ‘snowfall’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘DNAcopy:::getbdry’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘Biobase:::assayDataDims’ ‘DNAcopy:::trimmed.variance’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.MakeData’ ‘.alpha0all’ ‘.assignNames’ ‘.callFromSeg’ ‘.countcl’
  ‘.posteriorp’ ‘.reallik4’ ‘.segFromRaw’ ‘.sumreg’ ‘.sumsqreg’
  ‘.totallik’ ‘.varproffun’ ‘.varregtimescount’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.callFromSeg: no visible global function definition for ‘new’
.changepoints.sdundo2 : <anonymous>: no visible global function
  definition for ‘median’
.changepoints2: no visible global function definition for ‘mad’
.changepoints2: no visible global function definition for
  ‘changepoints.prune’
.makeEmptyFeatureData: no visible global function definition for ‘is’
.makeEmptyFeatureData: no visible global function definition for ‘new’
.profreg: no visible binding for global variable ‘profile’
.segFromRaw: no visible global function definition for ‘new’
.segment2: no visible binding for global variable
  ‘default.DNAcopy.bdry’
.totallik: no visible global function definition for ‘sfExport’
.totallik: no visible global function definition for ‘sfSapply’
.varregtimescount: no visible global function definition for ‘var’
CGHcall: no visible global function definition for ‘mad’
CGHcall: no visible global function definition for ‘sfInit’
CGHcall: no visible global function definition for ‘sfLibrary’
CGHcall: no visible global function definition for ‘sfExport’
CGHcall: no visible global function definition for ‘optim’
CGHcall: no visible global function definition for ‘sfRemoveAll’
CGHcall: no visible global function definition for ‘sfStop’
ExpandCGHcall: no visible global function definition for ‘new’
normalize: no visible global function definition for ‘median’
postsegnormalize: no visible global function definition for ‘median’
Undefined global functions or variables:
  changepoints.prune default.DNAcopy.bdry is mad median new optim
  profile sfExport sfInit sfLibrary sfRemoveAll sfSapply sfStop var
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "mad", "median", "optim", "profile", "var")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/CGHcall.Rcheck/00check.log’
for details.


Installation output

CGHcall.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CGHcall
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘CGHcall’ ...
** using staged installation
** R
** data
** 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 (CGHcall)

Tests output


Example timings

CGHcall.Rcheck/CGHcall-Ex.timings

nameusersystemelapsed
CGHcall0.2070.0080.215
ExpandCGHcall0.1530.0040.158
normalize0.1180.0000.117
postsegnormalize0.1150.0080.123
preprocess0.0360.0040.040
segmentData0.0180.0040.021