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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 1963/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIAMCAT 2.8.0  (landing page)
Jakob Wirbel
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/SIAMCAT
git_branch: RELEASE_3_19
git_last_commit: 2a7c890
git_last_commit_date: 2024-04-30 11:06:40 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SIAMCAT on nebbiolo1

To the developers/maintainers of the SIAMCAT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIAMCAT.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: SIAMCAT
Version: 2.8.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SIAMCAT_2.8.0.tar.gz
StartedAt: 2024-06-13 03:35:36 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 03:44:18 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 522.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SIAMCAT.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SIAMCAT_2.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SIAMCAT.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 ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SIAMCAT’ 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 ... 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 LazyData ... 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
make.predictions          32.841  0.296  33.136
assign-model_list         31.902  0.572  32.475
model.interpretation.plot 31.909  0.292  32.201
train.model               30.137  0.165  30.302
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.


Installation output

SIAMCAT.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘SIAMCAT’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (SIAMCAT)

Tests output


Example timings

SIAMCAT.Rcheck/SIAMCAT-Ex.timings

nameusersystemelapsed
accessSlot0.010.000.01
add.meta.pred0.4810.0800.560
assign-associations0.0060.0000.006
assign-data_split0.0060.0000.006
assign-eval_data0.0060.0000.006
assign-filt_feat0.0070.0000.007
assign-label0.0070.0000.006
assign-meta0.0210.0040.024
assign-model_list31.902 0.57232.475
assign-norm_feat0.0070.0000.006
assign-orig_feat0.0080.0040.012
assign-physeq0.0030.0040.007
assign-pred_matrix0.0070.0000.006
assoc_param-methods0.0050.0000.005
association.plot0.2140.0040.218
associations-methods0.0090.0000.009
check.associations0.010.000.01
check.confounders0.4220.0040.426
create.data.split0.020.000.02
create.label0.0020.0000.003
data_split-methods0.0040.0000.005
eval_data-methods0.0290.0000.029
evaluate.predictions1.4690.0441.513
feature_type-methods0.0010.0040.005
feature_weights-methods0.0050.0000.005
filt_feat-methods0.0050.0000.005
filt_params-methods0.0050.0000.005
filter.features0.0130.0000.013
filter.label0.0070.0000.006
get.filt_feat.matrix0.0050.0000.005
get.norm_feat.matrix0.0050.0000.005
get.orig_feat.matrix0.0050.0000.005
label-methods0.0050.0000.005
make.predictions32.841 0.29633.136
meta-methods0.0340.0030.039
model.evaluation.plot0.0300.0010.030
model.interpretation.plot31.909 0.29232.201
model_list-methods0.0050.0000.005
model_type-methods0.0040.0000.005
models-methods0.0050.0000.005
norm_feat-methods0.0050.0000.005
norm_params-methods0.0010.0030.005
normalize.features0.0120.0010.013
orig_feat-methods0.0010.0040.005
physeq-methods0.0070.0000.008
pred_matrix-methods0.0050.0000.006
read.label0.0060.0000.007
read.lefse0.4790.0070.489
select.samples0.0810.0010.082
siamcat0.2350.0150.249
siamcat.to.lefse0.0180.0030.022
siamcat.to.maaslin0.0240.0000.023
summarize.features1.4270.0161.443
train.model30.137 0.16530.302
validate.data0.0170.0000.017
volcano.plot0.0110.0000.010
weight_matrix-methods0.0000.0030.005