Sofie Van Gassen
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/FlowSOM |
| Branch: RELEASE_3_10 |
| Last Commit: 850e5b7 |
| Last Changed Date: 2019-10-29 13:09:07 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:41:14 -0400 (Wed, 15 Apr 2020).
| Package 599/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FlowSOM 1.18.0 Sofie Van Gassen
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: FlowSOM |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FlowSOM_1.18.0.tar.gz |
| StartedAt: 2020-04-15 02:22:58 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:27:32 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 273.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: FlowSOM.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FlowSOM_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/FlowSOM.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘1.18.0’
* 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 ‘FlowSOM’ can be installed ... WARNING
Found the following significant warnings:
som.c:37:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
som.c:47:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
som.c:134:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/FlowSOM.Rcheck/00install.out’ for details.
* 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 ... NOTE
AddFlowFrame: no visible global function definition for ‘is’
ReadInput: no visible global function definition for ‘is’
Undefined global functions or variables:
is
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
PlotOverview2D 12.305 0.843 13.356
CountGroups 11.523 1.239 12.863
FlowSOM 8.860 0.885 9.827
PlotPies 5.921 0.492 6.464
MetaclusterMFIs 5.647 0.653 6.368
FlowSOMSubset 5.279 0.482 5.857
MetaclusterCVs 5.195 0.501 5.753
TestOutliers 5.048 0.620 5.701
GetFlowJoLabels 5.161 0.479 5.692
GetMetaclusters 5.098 0.421 5.579
GetClusters 4.730 0.484 5.259
PlotLabels 4.655 0.454 5.155
GetMFIs 4.557 0.474 5.097
MetaClustering 4.495 0.472 5.109
* 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 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.
FlowSOM.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c som.c -o som.o
som.c:37:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
xdist += abs(tmp);
^
som.c:37:18: note: use function 'fabs' instead
xdist += abs(tmp);
^~~
fabs
som.c:47:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
tmp = abs(tmp);
^
som.c:47:15: note: use function 'fabs' instead
tmp = abs(tmp);
^~~
fabs
som.c:134:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
change += abs(tmp);
^
som.c:134:27: note: use function 'fabs' instead
change += abs(tmp);
^~~
fabs
3 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-FlowSOM/00new/FlowSOM/libs
** R
** 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 (FlowSOM)
FlowSOM.Rcheck/FlowSOM-Ex.timings
| name | user | system | elapsed | |
| AggregateFlowFrames | 0.469 | 0.027 | 0.503 | |
| BuildMST | 1.843 | 0.119 | 1.977 | |
| BuildSOM | 1.966 | 0.125 | 2.101 | |
| CountGroups | 11.523 | 1.239 | 12.863 | |
| FMeasure | 0.002 | 0.000 | 0.002 | |
| FlowSOM | 8.860 | 0.885 | 9.827 | |
| FlowSOMSubset | 5.279 | 0.482 | 5.857 | |
| GetClusters | 4.730 | 0.484 | 5.259 | |
| GetFlowJoLabels | 5.161 | 0.479 | 5.692 | |
| GetMFIs | 4.557 | 0.474 | 5.097 | |
| GetMetaclusters | 5.098 | 0.421 | 5.579 | |
| Initialize_KWSP | 0.008 | 0.000 | 0.008 | |
| Initialize_PCA | 0.002 | 0.000 | 0.003 | |
| MetaClustering | 4.495 | 0.472 | 5.109 | |
| MetaclusterCVs | 5.195 | 0.501 | 5.753 | |
| MetaclusterMFIs | 5.647 | 0.653 | 6.368 | |
| NewData | 4.259 | 0.389 | 4.704 | |
| PlotCenters | 1.426 | 0.131 | 1.564 | |
| PlotClusters2D | 1.283 | 0.094 | 1.383 | |
| PlotGroups | 0 | 0 | 0 | |
| PlotLabels | 4.655 | 0.454 | 5.155 | |
| PlotMarker | 1.339 | 0.105 | 1.449 | |
| PlotNode | 4.484 | 0.474 | 4.995 | |
| PlotNumbers | 1.384 | 0.092 | 1.486 | |
| PlotOverview2D | 12.305 | 0.843 | 13.356 | |
| PlotPies | 5.921 | 0.492 | 6.464 | |
| PlotSD | 1.567 | 0.092 | 1.669 | |
| PlotStars | 1.329 | 0.097 | 1.438 | |
| PlotVariable | 1.427 | 0.082 | 1.517 | |
| Purity | 0.001 | 0.000 | 0.001 | |
| QueryStarPlot | 3.493 | 0.164 | 3.686 | |
| ReadInput | 3.875 | 0.581 | 4.503 | |
| TestOutliers | 5.048 | 0.620 | 5.701 | |
| UpdateNodeSize | 1.465 | 0.106 | 1.585 | |
| get_channels | 0.046 | 0.005 | 0.052 | |
| get_markers | 0.059 | 0.008 | 0.068 | |
| metaClustering_consensus | 3.468 | 0.417 | 3.921 | |