Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:32 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 FEAST on tokay2


To the developers/maintainers of the FEAST package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FEAST.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 634/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FEAST 1.2.0  (landing page)
Kenong Su
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/FEAST
git_branch: RELEASE_3_14
git_last_commit: cf2e5e8
git_last_commit_date: 2021-10-26 13:09:07 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FEAST
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FEAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings FEAST_1.2.0.tar.gz
StartedAt: 2022-04-12 19:34:57 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:39:08 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 251.9 seconds
RetCode: 0
Status:   OK  
CheckDir: FEAST.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FEAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings FEAST_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/FEAST.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FEAST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FEAST' version '1.2.0'
* 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 'FEAST' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.5Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
FEAST: multiple local function definitions for 'bp_fun' with different
  formal arguments
SC3_Clust: no visible global function definition for 'metadata'
Visual_Rslt: no visible global function definition for 'ggbarplot'
Visual_Rslt: no visible global function definition for 'theme'
Visual_Rslt: no visible global function definition for 'element_text'
Visual_Rslt: no visible global function definition for 'ggline'
Visual_Rslt: no visible global function definition for 'get_palette'
Visual_Rslt: no visible global function definition for
  'scale_y_continuous'
Visual_Rslt: no visible global function definition for 'guides'
Visual_Rslt: no visible global function definition for 'guide_legend'
Visual_Rslt: no visible global function definition for 'ggarrange'
aricode_NMI : entropy: no visible global function definition for
  'sortPairs'
Undefined global functions or variables:
  element_text get_palette ggarrange ggbarplot ggline guide_legend
  guides metadata scale_y_continuous sortPairs theme
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/FEAST/libs/i386/FEAST.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/FEAST/libs/x64/FEAST.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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. 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/FEAST.Rcheck/00check.log'
for details.



Installation output

FEAST.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/FEAST_1.2.0.tar.gz && rm -rf FEAST.buildbin-libdir && mkdir FEAST.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FEAST.buildbin-libdir FEAST_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL FEAST_1.2.0.zip && rm FEAST_1.2.0.tar.gz FEAST_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 3581k    1 51217    0     0   329k      0  0:00:10 --:--:--  0:00:10  329k
 43 3581k   43 1552k    0     0  1354k      0  0:00:02  0:00:01  0:00:01 1353k
 90 3581k   90 3233k    0     0  1509k      0  0:00:02  0:00:02 --:--:-- 1509k
100 3581k  100 3581k    0     0  1538k      0  0:00:02  0:00:02 --:--:-- 1539k

install for i386

* installing *source* package 'FEAST' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c cal_3_metrics.c -o cal_3_metrics.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o FEAST.dll tmp.def cal_3_metrics.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/FEAST.buildbin-libdir/00LOCK-FEAST/00new/FEAST/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FEAST'
    finding HTML links ... done
    Consensus                               html  
    FEAST                                   html  
    FEAST_fast                              html  
    Norm_Y                                  html  
    Purity                                  html  
    SC3_Clust                               html  
    Select_Model_short_SC3                  html  
    Select_Model_short_TSCAN                html  
    TSCAN_Clust                             html  
    Visual_Rslt                             html  
    Y                                       html  
    align_CellType                          html  
    cal_F2                                  html  
    cal_Fisher2                             html  
    cal_MSE                                 html  
    cal_metrics                             html  
    eval_Cluster                            html  
    process_Y                               html  
    setUp_BPPARAM                           html  
    trueclass                               html  
    vector2matrix                           html  
** 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

install for x64

* installing *source* package 'FEAST' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c cal_3_metrics.c -o cal_3_metrics.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o FEAST.dll tmp.def cal_3_metrics.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/FEAST.buildbin-libdir/FEAST/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FEAST' as FEAST_1.2.0.zip
* DONE (FEAST)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'FEAST' successfully unpacked and MD5 sums checked

Tests output


Example timings

FEAST.Rcheck/examples_i386/FEAST-Ex.timings

nameusersystemelapsed
Consensus0.780.050.83
FEAST0.770.030.79
FEAST_fast1.020.051.07
Norm_Y0.640.060.70
Select_Model_short_SC30.340.020.36
Select_Model_short_TSCAN0.340.010.36
TSCAN_Clust000
Visual_Rslt1.020.061.08
Y0.090.020.11
align_CellType000
cal_F20.560.120.69
cal_MSE0.840.050.89
eval_Cluster000
process_Y0.190.000.19
setUp_BPPARAM000
trueclass0.000.020.01

FEAST.Rcheck/examples_x64/FEAST-Ex.timings

nameusersystemelapsed
Consensus0.820.010.85
FEAST0.880.040.90
FEAST_fast1.560.071.64
Norm_Y0.280.070.35
Select_Model_short_SC30.320.030.34
Select_Model_short_TSCAN0.320.030.36
TSCAN_Clust000
Visual_Rslt0.640.030.67
Y0.110.000.11
align_CellType0.020.000.02
cal_F21.250.081.33
cal_MSE0.970.051.01
eval_Cluster000
process_Y0.140.010.15
setUp_BPPARAM0.020.000.02
trueclass000