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This page was generated on 2025-01-23 12:06 -0500 (Thu, 23 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4493
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4394
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 2106/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SynExtend 1.18.0  (landing page)
Nicholas Cooley
Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 2025)
git_url: https://git.bioconductor.org/packages/SynExtend
git_branch: RELEASE_3_20
git_last_commit: 75461e3
git_last_commit_date: 2024-10-29 10:46:40 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
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    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SynExtend on nebbiolo2

To the developers/maintainers of the SynExtend package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SynExtend.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: SynExtend
Version: 1.18.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SynExtend_1.18.0.tar.gz
StartedAt: 2025-01-21 02:44:48 -0500 (Tue, 21 Jan 2025)
EndedAt: 2025-01-21 02:52:25 -0500 (Tue, 21 Jan 2025)
EllapsedTime: 457.6 seconds
RetCode: 0
Status:   OK  
CheckDir: SynExtend.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SynExtend_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SynExtend.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ 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 ‘SynExtend’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘DECIPHER:::.detectCores’
  See the note in ?`:::` about the use of this operator.
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking usage of KIND in Fortran files ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
BuiltInEnsembles        86.503  0.244  86.751
BlockExpansion          71.995  0.835  72.836
ExampleStreptomycesData 60.783  0.139  60.923
SelectByK               43.899  0.317  44.217
ExpandDiagonal          25.290  0.539  25.830
SummarizePairs          13.025  0.500  13.527
predict.EvoWeaver        7.982  0.000   7.982
gffToDataFrame           5.566  0.000   5.567
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/SynExtend.Rcheck/00check.log’
for details.


Installation output

SynExtend.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SynExtend
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘SynExtend’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c CDend.c -o CDend.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c CShuffle.c -o CShuffle.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c HungarianAlgo.c -o HungarianAlgo.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c MoranI.c -o MoranI.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c NucleotideCounts.c -o NucleotideCounts.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c OnDiskLP.c -o OnDiskLP.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c PrefixTrie.c -o PrefixTrie.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c R_init_synextend.c -o R_init_synextend.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c RandomForest.c -o RandomForest.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c SEutils.c -o SEutils.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c XORRand.c -o XORRand.o
gfortran  -fpic  -g -O2  -Wall -c  _fortran_tabulate.f95 -o _fortran_tabulate.o
gfortran  -fpic  -g -O2  -Wall -c  _fortran_utils.f95 -o _fortran_utils.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c calcMIR2C.c -o calcMIR2C.o
gfortran  -fpic  -g -O2  -Wall -c  cart_fort.f95 -o cart_fort.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c dendrapply.c -o dendrapply.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o SynExtend.so CDend.o CShuffle.o HungarianAlgo.o MoranI.o NucleotideCounts.o OnDiskLP.o PrefixTrie.o R_init_synextend.o RandomForest.o SEutils.o XORRand.o _fortran_tabulate.o _fortran_utils.o calcMIR2C.o cart_fort.o dendrapply.o -fopenmp -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-SynExtend/00new/SynExtend/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 (SynExtend)

Tests output


Example timings

SynExtend.Rcheck/SynExtend-Ex.timings

nameusersystemelapsed
BlastSeqs000
BlockExpansion71.995 0.83572.836
BlockReconciliation000
BuiltInEnsembles86.503 0.24486.751
CIDist_NullDist0.0020.0000.002
ClusterByK3.0920.0113.103
DPhyloStatistic0.0320.0020.033
DecisionTree-class0.0350.0040.039
DisjointSet0.0810.0030.084
Endosymbionts_GeneCalls0.0090.0010.010
Endosymbionts_LinkedFeatures0.0250.0020.027
Endosymbionts_Pairs010.0230.0000.023
Endosymbionts_Pairs020.0230.0000.023
Endosymbionts_Pairs030.0190.0020.022
Endosymbionts_Sets0.0020.0010.003
Endosymbionts_Synteny0.0130.0010.014
EstimRearrScen1.3330.0161.349
EstimateExoLabel0.0020.0000.002
EvoWeaver0.0020.0000.003
EvoWeb0.0310.0010.032
ExampleStreptomycesData60.783 0.13960.923
ExoLabel0.0160.0010.017
ExpandDiagonal25.290 0.53925.830
ExtractBy0.2720.0020.275
FastQFromSRR000
FindSets0.0010.0000.001
FitchParsimony0.0600.0010.061
Generic0.0020.0000.002
MakeBlastDb000
MoransI000
NucleotideOverlap0.9820.0010.983
PairSummaries3.1150.0063.121
PhyloDistance-CI0.0040.0000.004
PhyloDistance-JRF0.0030.0000.002
PhyloDistance-KF0.0020.0000.001
PhyloDistance-RF0.0020.0000.001
PhyloDistance0.0020.0000.003
PrepareSeqs0.0280.0000.027
RandForest0.0130.0000.013
SelectByK43.899 0.31744.217
SequenceSimilarity0.0650.0020.068
SubSetPairs0.4010.0050.406
SummarizePairs13.025 0.50013.527
SuperTree0.1890.0000.189
SuperTreeEx0.0080.0000.008
dendrapply0.0900.0000.089
gffToDataFrame5.5660.0005.567
plot.EvoWeb0.9170.0090.926
predict.EvoWeaver7.9820.0007.982
simMat0.0150.0000.015
subset-dendrogram0.3290.0050.334