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This page was generated on 2022-01-22 11:06:01 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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

CHECK results for IRISFGM on nebbiolo1


To the developers/maintainers of the IRISFGM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IRISFGM.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 953/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRISFGM 1.3.0  (landing page)
Yuzhou Chang
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/IRISFGM
git_branch: master
git_last_commit: 801cde9
git_last_commit_date: 2021-10-26 13:07:08 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'clusterProfiler' which is not available

Summary

Package: IRISFGM
Version: 1.3.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:IRISFGM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings IRISFGM_1.3.0.tar.gz
StartedAt: 2022-01-21 19:40:35 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 19:45:55 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 320.7 seconds
RetCode: 0
Status:   OK  
CheckDir: IRISFGM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:IRISFGM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings IRISFGM_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/IRISFGM.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRISFGM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IRISFGM’ version ‘1.3.0’
* 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 ‘IRISFGM’ 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 R 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 ... 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 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
RunDimensionReduction 5.853  0.844   6.698
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/IRISFGM.Rcheck/00check.log’
for details.



Installation output

IRISFGM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL IRISFGM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘IRISFGM’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -DVER=2.08 -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -DVER=2.08 -fpic  -g -O2  -Wall -c cluster.cpp -o cluster.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -DVER=2.08 -fpic  -g -O2  -Wall -c expand.cpp -o expand.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -DVER=2.08 -fpic  -g -O2  -Wall -c get_options.cpp -o get_options.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getline.c -o getline.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -DVER=2.08 -fpic  -g -O2  -Wall -c main.cpp -o main.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -DVER=2.08 -fpic  -g -O2  -Wall -c make_graph.cpp -o make_graph.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -DVER=2.08 -fpic  -g -O2  -Wall -c rcpp_irisfgm.cpp -o rcpp_irisfgm.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -DVER=2.08 -fpic  -g -O2  -Wall -c read_array.cpp -o read_array.o
read_array.cpp: In function ‘void discretize_new(const char*)’:
read_array.cpp:882:26: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=]
  882 |         fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
      |                         ~^
      |                          |
      |                          int
      |                         %ld
read_array.cpp:883:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  883 |         for (std::size_t j = 0; j < cols; j++) {
      |                                 ~~^~~~~~
read_array.cpp: In function ‘void discretize_rpkm(const char*)’:
read_array.cpp:1376:26: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=]
 1376 |         fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
      |                         ~^
      |                          |
      |                          int
      |                         %ld
read_array.cpp:1377:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1377 |         for (std::size_t j = 0; j < cols; j++) {
      |                                 ~~^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -DVER=2.08 -fpic  -g -O2  -Wall -c struct.cpp -o struct.o
struct.cpp: In function ‘void uglyTime(const char*, ...)’:
struct.cpp:75:15: warning: variable ‘lastTime’ set but not used [-Wunused-but-set-variable]
   75 |   static long lastTime = 0;
      |               ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -DVER=2.08 -fpic  -g -O2  -Wall -c write_block.cpp -o write_block.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o IRISFGM.so RcppExports.o cluster.o expand.o get_options.o getline.o main.o make_graph.o rcpp_irisfgm.o read_array.o struct.o write_block.o -fopenmp -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-IRISFGM/00new/IRISFGM/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘ReadFrom10X_h5’ in package ‘IRISFGM’
Creating a generic function from function ‘ReadFrom10X_folder’ in package ‘IRISFGM’
** 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 (IRISFGM)

Tests output


Example timings

IRISFGM.Rcheck/IRISFGM-Ex.timings

nameusersystemelapsed
AddMeta0.0050.0000.004
CalBinaryMultiSignal0.3150.0000.314
CalBinarySingleSignal0.2200.0120.232
CreateIRISFGMObject0.0020.0000.002
DotPlotPathway0.2090.0000.208
FindClassBasedOnMC2.8980.0482.946
FindGlobalMarkers2.0020.0162.018
FindMarker0.2050.0000.205
GetBinaryMultiSignal0.2050.0080.213
GetBinarySingleSignal0.2070.0040.210
GetLTMGmatrix0.2070.0040.211
PlotDimension0.3940.0040.399
PlotHeatmap0.3140.0120.327
PlotMarkerHeatmap0.8860.0390.925
PlotMeta0.3080.0040.312
PlotModuleNetwork1.1920.0801.271
PlotNetwork0.6600.0080.668
ProcessData0.2190.0040.223
RunBicluster2.9320.0923.024
RunClassification0.4790.0160.495
RunDimensionReduction5.8530.8446.698
RunDiscretization0.2470.0080.255
RunLTMG2.8610.3883.249
RunPathway0.2080.0070.215
SubsetData0.2060.0040.210
getMeta0.2030.0120.215