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This page was generated on 2024-12-24 11:44 -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 2090/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SynExtend 1.19.0  (landing page)
Nicholas Cooley
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/SynExtend
git_branch: devel
git_last_commit: fbefdf6
git_last_commit_date: 2024-12-03 12:04:30 -0500 (Tue, 03 Dec 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 SynExtend on lconway

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: 1.19.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SynExtend_1.19.0.tar.gz
StartedAt: 2024-12-23 23:33:55 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 23:42:51 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 536.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SynExtend.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SynExtend_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SynExtend.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.19.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BlockExpansion.Rd: FindSynteny
  BlockReconciliation.Rd: FindSynteny, Synteny-class
  ClusterByK.Rd: FindSynteny
  DisjointSet.Rd: FindSynteny, Synteny-class
  EstimRearrScen.Rd: Synteny-class, FindSynteny
  ExpandDiagonal.Rd: AlignPairs, FindSynteny
  ExtractBy.Rd: FindSynteny, Synteny-class
  NucleotideOverlap.Rd: FindSynteny, Synteny-class
  PairSummaries.Rd: FindSynteny, Synteny-class
  PrepareSeqs.Rd: FindSynteny
  SelectByK.Rd: FindSynteny
  SequenceSimilarity.Rd: AlignSeqs, AlignProfiles, AlignTranslation,
    DistanceMatrix
  SummarizePairs.Rd: SearchIndex, AlignProfiles, AlignPairs,
    FindSynteny, IndexSeqs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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        96.803  2.896 100.365
BlockExpansion          88.809  1.284  90.639
ExampleStreptomycesData 69.758  1.499  71.778
SelectByK               54.978  1.040  56.369
ExpandDiagonal          29.091  1.045  30.401
SummarizePairs          15.925  0.542  16.594
predict.EvoWeaver        8.687  0.236   8.976
gffToDataFrame           7.208  0.060   7.304
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/SynExtend.Rcheck/00check.log’
for details.


Installation output

SynExtend.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SynExtend
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SynExtend’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c CDend.c -o CDend.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c CShuffle.c -o CShuffle.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c HungarianAlgo.c -o HungarianAlgo.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c MoranI.c -o MoranI.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c NucleotideCounts.c -o NucleotideCounts.o
NucleotideCounts.c:267:7: warning: unused variable 'nthreads' [-Wunused-variable]
  int nthreads = INTEGER(NTHREADS)[0];
      ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c OnDiskLP.c -o OnDiskLP.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PrefixTrie.c -o PrefixTrie.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_synextend.c -o R_init_synextend.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RandomForest.c -o RandomForest.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c SEutils.c -o SEutils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XORRand.c -o XORRand.o
XORRand.c:67:7: warning: unused variable 'threads' [-Wunused-variable]
  int threads = INTEGER(NTHREADS)[0];
      ^
1 warning generated.
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c  _fortran_tabulate.f95 -o _fortran_tabulate.o
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c  _fortran_utils.f95 -o _fortran_utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c calcMIR2C.c -o calcMIR2C.o
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c  cart_fort.f95 -o cart_fort.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c dendrapply.c -o dendrapply.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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
BlastSeqs0.0000.0000.001
BlockExpansion88.809 1.28490.639
BlockReconciliation0.0000.0010.000
BuiltInEnsembles 96.803 2.896100.365
CIDist_NullDist0.0010.0020.005
ClusterByK3.1540.0343.210
DPhyloStatistic0.0400.0030.044
DecisionTree-class0.0420.0020.048
DisjointSet0.0930.0050.106
Endosymbionts_GeneCalls0.0100.0020.013
Endosymbionts_LinkedFeatures0.0270.0010.029
Endosymbionts_Pairs010.0260.0030.029
Endosymbionts_Pairs020.0300.0030.033
Endosymbionts_Pairs030.0270.0030.029
Endosymbionts_Sets0.0030.0010.005
Endosymbionts_Synteny0.0140.0020.017
EstimRearrScen1.7970.0351.857
EstimateExoLabel0.0020.0010.004
EvoWeaver0.0030.0010.005
EvoWeb0.0430.0080.055
ExampleStreptomycesData69.758 1.49971.778
ExoLabel0.0190.0120.032
ExpandDiagonal29.091 1.04530.401
ExtractBy0.2970.0080.307
FastQFromSRR000
FindSets0.0020.0010.002
FitchParsimony0.0770.0050.084
Generic0.0020.0020.004
MakeBlastDb000
MoransI0.0000.0000.002
NucleotideOverlap1.4210.0381.466
PairSummaries3.5320.0733.621
PhyloDistance-CI0.0040.0010.006
PhyloDistance-JRF0.0040.0000.006
PhyloDistance-KF0.0020.0000.002
PhyloDistance-RF0.0030.0010.003
PhyloDistance0.0040.0010.005
PrepareSeqs0.0270.0020.029
RandForest0.0150.0020.016
SelectByK54.978 1.04056.369
SequenceSimilarity0.0660.0030.071
SubSetPairs0.4980.0590.561
SummarizePairs15.925 0.54216.594
SuperTree0.2290.0070.238
SuperTreeEx0.0130.0010.014
dendrapply0.1200.0150.135
gffToDataFrame7.2080.0607.304
plot.EvoWeb0.9410.0330.979
predict.EvoWeaver8.6870.2368.976
simMat0.0170.0040.021
subset-dendrogram0.3840.0110.398