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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 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 2061/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SynExtend 1.17.0  (landing page)
Nicholas Cooley
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/SynExtend
git_branch: devel
git_last_commit: 7cdfb94
git_last_commit_date: 2024-04-30 11:23:46 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for SynExtend on palomino4

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: 1.17.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SynExtend.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SynExtend_1.17.0.tar.gz
StartedAt: 2024-06-10 10:56:13 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 11:09:16 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 783.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SynExtend.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SynExtend.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SynExtend_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SynExtend.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SynExtend/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SynExtend' version '1.17.0'
* 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 whether package 'SynExtend' can be installed ... WARNING
Found the following significant warnings:
  OnDiskLP.c:947:42: warning: overflow in conversion from 'long long unsigned int' to 'long int' changes value from '18446744073709551608' to '-8' [-Woverflow]
  OnDiskLP.c:1380:44: warning: overflow in conversion from 'long long unsigned int' to 'long int' changes value from '18446744073709551608' to '-8' [-Woverflow]
See 'F:/biocbuild/bbs-3.20-bioc/meat/SynExtend.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 dependencies in R code ... WARNING
'library' or 'require' call not declared from: 'RSQLite'
'library' or 'require' call to 'RSQLite' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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 ... NOTE
prepare_Rd: EstimateExoLabel.Rd:41-43: Dropping empty section \references
checkRd: (-1) ExampleStreptomycesData.Rd:8: Lost braces; missing escapes or markup?
     8 | Data from {Streptomyces} species to test \code{\link{EvoWeaver}} functionality.
       |           ^
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/SynExtend/libs/x64/SynExtend.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
ExpandDiagonal    85.45  10.26   95.74
BlockExpansion    85.42   9.05   94.59
SelectByK         54.03   6.31   60.36
SummarizePairs    50.92   5.85   56.76
predict.EvoWeaver 13.34   2.00   20.71
BuiltInEnsembles  11.86   1.84   18.14
gffToDataFrame     6.79   0.07    6.86
* 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 WARNINGs, 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/SynExtend.Rcheck/00check.log'
for details.


Installation output

SynExtend.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SynExtend
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'SynExtend' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CDend.c -o CDend.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CShuffle.c -o CShuffle.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c HungarianAlgo.c -o HungarianAlgo.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MoranI.c -o MoranI.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c NucleotideCounts.c -o NucleotideCounts.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c OnDiskLP.c -o OnDiskLP.o
OnDiskLP.c: In function 'normalize_csr_edgecounts':
OnDiskLP.c:947:42: warning: overflow in conversion from 'long long unsigned int' to 'long int' changes value from '18446744073709551608' to '-8' [-Woverflow]
  947 |                         fseek(mastertab, -1*sizeof(double), SEEK_CUR);
      |                                          ^~~~~~~~~~~~~~~~~
OnDiskLP.c: In function 'resolve_cluster_consensus':
OnDiskLP.c:1380:44: warning: overflow in conversion from 'long long unsigned int' to 'long int' changes value from '18446744073709551608' to '-8' [-Woverflow]
 1380 |                                 fseek(csr, -1*sizeof(double), SEEK_CUR);
      |                                            ^~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_synextend.c -o R_init_synextend.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SEutils.c -o SEutils.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XORRand.c -o XORRand.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c calcMIR2C.c -o calcMIR2C.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dendrapply.c -o dendrapply.o
gcc -shared -s -static-libgcc -o SynExtend.dll tmp.def CDend.o CShuffle.o HungarianAlgo.o MoranI.o NucleotideCounts.o OnDiskLP.o R_init_synextend.o SEutils.o XORRand.o calcMIR2C.o dendrapply.o -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-SynExtend/00new/SynExtend/libs/x64
** 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
** 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
BlockExpansion85.42 9.0594.59
BlockReconciliation000
BuiltInEnsembles11.86 1.8418.14
CIDist_NullDist0.020.000.01
ClusterByK2.840.032.88
DPhyloStatistic0.050.000.05
DisjointSet0.110.020.12
Endosymbionts_GeneCalls0.000.030.03
Endosymbionts_LinkedFeatures0.030.000.03
Endosymbionts_Pairs010.020.010.04
Endosymbionts_Pairs020.030.000.03
Endosymbionts_Pairs030.030.000.03
Endosymbionts_Sets0.000.020.01
Endosymbionts_Synteny0.010.010.03
EstimRearrScen1.740.161.90
EstimateExoLabel000
EvoWeaver0.010.000.01
EvoWeb0.070.000.06
ExampleStreptomycesData1.010.131.14
ExoLabel0.000.000.21
ExpandDiagonal85.4510.2695.74
ExtractBy0.310.030.34
FastQFromSRR000
FindSets000
FitchParsimony0.070.000.06
Generic0.000.020.02
MakeBlastDb000
MoransI000
NucleotideOverlap1.070.041.12
PairSummaries4.500.324.82
PhyloDistance-CI0.000.010.01
PhyloDistance-JRF000
PhyloDistance-KF000
PhyloDistance-RF000
PhyloDistance0.020.000.02
PrepareSeqs2.250.082.33
SelectByK54.03 6.3160.36
SequenceSimilarity0.090.020.10
SubSetPairs0.410.120.54
SummarizePairs50.92 5.8556.76
SuperTree0.690.010.70
SuperTreeEx0.060.000.07
dendrapply0.100.000.09
gffToDataFrame6.790.076.86
plot.EvoWeb0.550.030.58
predict.EvoWeaver13.34 2.0020.71
simMat000
subset-dendrogram0.050.000.04