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This page was generated on 2024-07-19 17:37 -0400 (Fri, 19 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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 1544/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PERFect 1.18.0  (landing page)
Quy Cao
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/PERFect
git_branch: RELEASE_3_19
git_last_commit: 80a0b6f
git_last_commit_date: 2024-04-30 11:18:06 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    NA  


CHECK results for PERFect on nebbiolo1

To the developers/maintainers of the PERFect package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PERFect.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: PERFect
Version: 1.18.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PERFect.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PERFect_1.18.0.tar.gz
StartedAt: 2024-07-18 02:48:31 -0400 (Thu, 18 Jul 2024)
EndedAt: 2024-07-18 02:50:54 -0400 (Thu, 18 Jul 2024)
EllapsedTime: 143.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: PERFect.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PERFect.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PERFect_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/PERFect.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘PERFect/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PERFect’ version ‘1.18.0’
* package encoding: UTF-8
* 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 ‘PERFect’ 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) DiffFiltLoss.Rd:28: Lost braces; missing escapes or markup?
    28 | for removing the first j taxa as DFL(j+1) = FL(J_{j+1}) - FL(J_j) for taxa j=1, ..., p.
       |                                                  ^
checkRd: (-1) FiltLoss.Rd:38: Lost braces; missing escapes or markup?
    38 | FL_u(j)= 1- (||X^T_{-j} X_{-j}||_F^2/||X^TX||_F^2),
       |                    ^
checkRd: (-1) FiltLoss.Rd:38: Lost braces; missing escapes or markup?
    38 | FL_u(j)= 1- (||X^T_{-j} X_{-j}||_F^2/||X^TX||_F^2),
       |                           ^
checkRd: (-1) FiltLoss.Rd:40: Lost braces; missing escapes or markup?
    40 | where X_{-j} is the matrix X without column corresponding to jth taxon and ||Z||_F is the Frobenious norm of a matrix Z.
       |         ^
checkRd: (-1) FiltLoss.Rd:44: Lost braces; missing escapes or markup?
    44 | FL(J)= 1- (||X^T_{-J}  X_{-J}||_F^2\||X^TX||_F^2),
       |                  ^
checkRd: (-1) FiltLoss.Rd:44: Lost braces; missing escapes or markup?
    44 | FL(J)= 1- (||X^T_{-J}  X_{-J}||_F^2\||X^TX||_F^2),
       |                          ^
checkRd: (-1) FiltLoss.Rd:46: Lost braces; missing escapes or markup?
    46 | where X_{-J} is the n x (p-|J|) dimensional matrix obtained by removing the columns indexed by the set J from the data matrix X.
       |         ^
* 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 ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘MethodIllustration.Rmd’ using rmarkdown
Error: processing vignette 'MethodIllustration.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘MethodIllustration.Rmd’

SUMMARY: processing the following file failed:
  ‘MethodIllustration.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/PERFect.Rcheck/00check.log’
for details.


Installation output

PERFect.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL PERFect
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘PERFect’ ...
** using staged installation
** 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
Warning in fun(libname, pkgname) :
  Package 'PERFect' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'PERFect' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (PERFect)

Tests output


Example timings

PERFect.Rcheck/PERFect-Ex.timings

nameusersystemelapsed
DiffFiltLoss0.1970.0120.209
FL_J0.0040.0040.008
FiltLoss0.1420.0040.145
NC_Order0.0070.0000.007
NCw_Order0.0070.0000.007
NP_Order0.0050.0000.006
PERFect_perm0.5840.0240.609
PERFect_perm_reorder0.0050.0000.005
PERFect_sim1.1330.0881.221
TraditR10.0070.0000.007
TraditR20.0050.0040.009
pvals_Order0.5130.0080.521
pvals_Plots0.8150.0000.816