Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1473/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Oscope 1.37.0  (landing page)
Ning Leng
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/Oscope
git_branch: devel
git_last_commit: 4ad579a
git_last_commit_date: 2024-10-29 10:02:50 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for Oscope on kunpeng2

To the developers/maintainers of the Oscope package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Oscope.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: Oscope
Version: 1.37.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Oscope.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Oscope_1.37.0.tar.gz
StartedAt: 2024-12-24 09:35:02 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 09:36:35 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 93.2 seconds
RetCode: 0
Status:   OK  
CheckDir: Oscope.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Oscope.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Oscope_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Oscope.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Oscope/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Oscope’ version ‘1.37.0’
* 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 ‘Oscope’ 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 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 ... 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 ... NOTE
AbsCor: no visible global function definition for ‘cor’
CalcMV: no visible binding for global variable ‘median’
CalcMV: no visible global function definition for ‘lm’
CalcMV: no visible global function definition for ‘coef’
CalcMV: no visible global function definition for ‘lines’
CalcMV: no visible global function definition for ‘points’
CalcMV: no visible global function definition for ‘abline’
FlagCluster: no visible global function definition for ‘quantile’
ImpShift: no visible global function definition for ‘txtProgressBar’
ImpShift: no visible global function definition for ‘setTxtProgressBar’
NISFun: no visible global function definition for ‘str’
NormForSine : <anonymous>: no visible global function definition for
  ‘quantile’
PipeR : <anonymous>: no visible global function definition for
  ‘residuals’
PipeR : <anonymous>: no visible global function definition for ‘lm’
PipeShiftCDF : <anonymous>: no visible global function definition for
  ‘quantile’
PipeShiftCDF : <anonymous>: no visible global function definition for
  ‘ecdf’
SineOptim: no visible global function definition for ‘optim’
scanK: no visible global function definition for ‘quantile’
scanK: no visible global function definition for ‘dist’
scanK : <anonymous>: no visible global function definition for ‘median’
Undefined global functions or variables:
  abline coef cor dist ecdf lines lm median optim points quantile
  residuals setTxtProgressBar str txtProgressBar
Consider adding
  importFrom("graphics", "abline", "lines", "points")
  importFrom("stats", "coef", "cor", "dist", "ecdf", "lm", "median",
             "optim", "quantile", "residuals")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) SineOptim.Rd:15: Lost braces; missing escapes or markup?
    15 | epsilon_{g1,g2}^2 = sum_s [X_{g1,s}^2+X^2_{g2,s}
       |         ^
checkRd: (-1) SineOptim.Rd:15: Lost braces; missing escapes or markup?
    15 | epsilon_{g1,g2}^2 = sum_s [X_{g1,s}^2+X^2_{g2,s}
       |                              ^
checkRd: (-1) SineOptim.Rd:15: Lost braces; missing escapes or markup?
    15 | epsilon_{g1,g2}^2 = sum_s [X_{g1,s}^2+X^2_{g2,s}
       |                                           ^
checkRd: (-1) SineOptim.Rd:16: Lost braces; missing escapes or markup?
    16 |                           -2X_{g1,s}X_{g2,s} cos(phi_{g1,g2})-sin^2(phi_{g1,g2})]^2
       |                               ^
checkRd: (-1) SineOptim.Rd:16: Lost braces; missing escapes or markup?
    16 |                           -2X_{g1,s}X_{g2,s} cos(phi_{g1,g2})-sin^2(phi_{g1,g2})]^2
       |                                       ^
checkRd: (-1) SineOptim.Rd:16: Lost braces; missing escapes or markup?
    16 |                           -2X_{g1,s}X_{g2,s} cos(phi_{g1,g2})-sin^2(phi_{g1,g2})]^2
       |                                                      ^
checkRd: (-1) SineOptim.Rd:16: Lost braces; missing escapes or markup?
    16 |                           -2X_{g1,s}X_{g2,s} cos(phi_{g1,g2})-sin^2(phi_{g1,g2})]^2
       |                                                                         ^
* 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
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
OscopeENI 10.596  0.117  10.733
PermuCut   7.074  0.004   7.091
NISFun     5.429  0.083   5.567
Opt2Shift  5.066  0.022   5.322
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/Oscope.Rcheck/00check.log’
for details.


Installation output

Oscope.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Oscope
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘Oscope’ ...
** using staged installation
** R
** data
** demo
** 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 (Oscope)

Tests output


Example timings

Oscope.Rcheck/Oscope-Ex.timings

nameusersystemelapsed
AbsCor0.0010.0000.001
CalcMV0.8550.0790.942
FlagCluster1.7640.0161.784
FormatSineOut0.0750.0000.075
ImpShift2.7500.0042.771
NISFun5.4290.0835.567
NormForSine0.090.000.09
Opt2Shift5.0660.0225.322
OscopeENI10.596 0.11710.733
OscopeExampleData0.0070.0000.007
OscopeKM1.1610.0241.187
OscopeSine0.1390.0040.142
PermuCut7.0740.0047.091
PipeR0.0050.0000.006
PipeShiftCDF0.0410.0000.041
SineFun0.0020.0000.002
SineOptim0.0010.0000.001
scanK1.0550.0521.109