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This page was generated on 2024-05-04 11:37:16 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 2121/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SynExtend 1.16.0  (landing page)
Nicholas Cooley
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/SynExtend
git_branch: RELEASE_3_19
git_last_commit: 4426e94
git_last_commit_date: 2024-04-30 11:23:46 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for SynExtend on nebbiolo1


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: 1.16.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SynExtend_1.16.0.tar.gz
StartedAt: 2024-05-04 04:14:37 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 04:21:29 -0400 (Sat, 04 May 2024)
EllapsedTime: 411.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SynExtend.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SynExtend_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SynExtend.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.16.0’
* 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 ... WARNING
Found the following significant warnings:
  OnDiskLP.c:1615:66: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
  OnDiskLP.c:382:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  OnDiskLP.c:572:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  OnDiskLP.c:758:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  OnDiskLP.c:759:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/SynExtend.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
BlockExpansion    70.155  1.019  71.179
ExpandDiagonal    69.233  0.656  69.890
SelectByK         51.536  0.320  51.857
SummarizePairs    41.492  0.244  41.736
predict.EvoWeaver 11.268  0.178  11.502
BuiltInEnsembles  10.699  0.084  10.825
gffToDataFrame     5.787  0.012   5.799
* 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 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SynExtend.Rcheck/00check.log’
for details.


Installation output

SynExtend.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SynExtend
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘SynExtend’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c CDend.c -o CDend.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c CShuffle.c -o CShuffle.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c HungarianAlgo.c -o HungarianAlgo.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c MoranI.c -o MoranI.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c NucleotideCounts.c -o NucleotideCounts.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c OnDiskLP.c -o OnDiskLP.o
OnDiskLP.c: In function ‘R_LP_write_output’:
OnDiskLP.c:1615:66: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
 1615 |                 snprintf(write_buf, (name_len+3)+L_SIZE, "%s%c%llu%c", buf, seps[0], clust, seps[1]);
      |                                                               ~~~^                   ~~~~~
      |                                                                  |                   |
      |                                                                  |                   uint_fast64_t {aka long unsigned int}
      |                                                                  long long unsigned int
      |                                                               %lu
OnDiskLP.c: In function ‘postcopy_vertexname’:
OnDiskLP.c:382:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  382 |         fread(cur_elem, sizeof(msort_vertex_line), 1, orig);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
OnDiskLP.c: In function ‘copy_csrfile_sig’:
OnDiskLP.c:572:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  572 |                 fread(&wbuf[cachectr], sizeof(double), 1, fs);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
OnDiskLP.c: In function ‘lookup_node_index’:
OnDiskLP.c:758:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  758 |                         fread(&tmplen, LEN_SIZE, 1, fhash);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
OnDiskLP.c:759:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  759 |                         fread(vname, 1, tmplen, fhash);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c SEutils.c -o SEutils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c XORRand.c -o XORRand.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c calcMIR2C.c -o calcMIR2C.o
gcc -I"/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -L/usr/local/lib -o SynExtend.so 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 -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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
BlockExpansion70.155 1.01971.179
BlockReconciliation000
BuiltInEnsembles10.699 0.08410.825
CIDist_NullDist0.0010.0000.002
ClusterByK3.2430.0003.244
DPhyloStatistic0.0290.0040.033
DisjointSet0.0740.0040.078
Endosymbionts_GeneCalls0.0110.0000.011
Endosymbionts_LinkedFeatures0.0270.0000.028
Endosymbionts_Pairs010.0200.0040.024
Endosymbionts_Pairs020.0240.0000.024
Endosymbionts_Pairs030.0190.0040.022
Endosymbionts_Sets0.0040.0000.003
Endosymbionts_Synteny0.0140.0000.013
EstimRearrScen1.3760.0321.409
EstimateExoLabel0.0000.0000.001
EvoWeaver0.0000.0030.003
EvoWeb0.0740.0010.075
ExampleStreptomycesData1.2340.1051.360
ExoLabel0.0110.0040.015
ExpandDiagonal69.233 0.65669.890
ExtractBy0.2800.0080.288
FastQFromSRR0.0000.0000.001
FindSets0.0020.0000.001
FitchParsimony0.0670.0000.067
Generic0.0020.0000.003
MakeBlastDb000
MoransI0.0020.0000.001
NucleotideOverlap1.2410.0201.260
PairSummaries2.6190.0082.627
PhyloDistance-CI0.0040.0000.004
PhyloDistance-JRF0.0030.0000.003
PhyloDistance-KF0.0020.0000.001
PhyloDistance-RF0.0020.0000.002
PhyloDistance0.0030.0000.003
PrepareSeqs1.4800.0041.484
SelectByK51.536 0.32051.857
SequenceSimilarity0.0740.0000.075
SubSetPairs0.4520.0000.452
SummarizePairs41.492 0.24441.736
SuperTree0.6310.0000.631
SuperTreeEx0.0710.0000.071
dendrapply0.0930.0040.097
gffToDataFrame5.7870.0125.799
plot.EvoWeb0.4760.0080.484
predict.EvoWeaver11.268 0.17811.502
simMat0.0250.0040.029
subset-dendrogram0.0380.0000.038