Greg Finak
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/flowClust |
| Branch: RELEASE_3_12 |
| Last Commit: 12da966 |
| Last Changed Date: 2020-10-27 10:33:06 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:18 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the flowClust package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 616/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowClust 3.28.0 (landing page) Greg Finak
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: flowClust |
| Version: 3.28.0 |
| Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/flowClust_3.28.0.tar.gz && rm -rf flowClust.buildbin-libdir && mkdir flowClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowClust.buildbin-libdir flowClust_3.28.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL flowClust_3.28.0.zip && rm flowClust_3.28.0.tar.gz flowClust_3.28.0.zip |
| StartedAt: 2021-05-05 17:52:24 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 17:52:58 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 33.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/flowClust_3.28.0.tar.gz && rm -rf flowClust.buildbin-libdir && mkdir flowClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowClust.buildbin-libdir flowClust_3.28.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL flowClust_3.28.0.zip && rm flowClust_3.28.0.tar.gz flowClust_3.28.0.zip
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install for i386
* installing *source* package 'flowClust' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BoxCox.c -o BoxCox.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BoxCoxPriors.c -o BoxCoxPriors.o
BoxCoxPriors.c: In function 'BoxCoxGradientPriors':
BoxCoxPriors.c:57:16: warning: unused variable 'rowZ' [-Wunused-variable]
rowPrecision, rowZ, rowLambda0;
^~~~
BoxCoxPriors.c:33:24: warning: unused variable 'kappa0' [-Wunused-variable]
double *nu0 = p->nu0, kappa0 = p->kappa0;
^~~~~~
BoxCoxPriors.c:32:7: warning: unused variable 'itersolve' [-Wunused-variable]
int *itersolve = p->itersolve;
^~~~~~~~~
BoxCoxPriors.c:31:6: warning: unused variable 'iter' [-Wunused-variable]
int iter = p->iter;
^~~~
BoxCoxPriors.c:28:6: warning: unused variable 'model' [-Wunused-variable]
int model = *p->model;
^~~~~
BoxCoxPriors.c:23:14: warning: unused variable 'SumZlogY' [-Wunused-variable]
gsl_vector *SumZlogY = p->SumZlogY;
^~~~~~~~
BoxCoxPriors.c:15:14: warning: unused variable 'Precision' [-Wunused-variable]
gsl_matrix *Precision = p->Precision; // will be updated
^~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Nu.c -o Nu.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flowClust.c -o flowClust.o
flowClust.c: In function 'flowClust':
flowClust.c:48:2: warning: unused variable 'matrixZUY2' [-Wunused-variable]
matrixZUY2;
^~~~~~~~~~
flowClust.c:46:48: warning: unused variable 'subRowZUY2' [-Wunused-variable]
rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
^~~~~~~~~~
flowClust.c:46:39: warning: unused variable 'rowZUY2' [-Wunused-variable]
rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
^~~~~~~
flowClust.c: In function 'ECMUpdateSigmaG2':
flowClust.c:1111:6: warning: unused variable 'i' [-Wunused-variable]
int i=0;
^
At top level:
flowClust.c:10:27: warning: 'CEntries' defined but not used [-Wunused-const-variable=]
static const R_CMethodDef CEntries[] = { { "flowClust", (DL_FUNC) & flowClust,
^~~~~~~~
flowClust.c: In function 'flowClust':
flowClust.c:702:13: warning: 's3' may be used uninitialized in this function [-Wmaybe-uninitialized]
status = gsl_min_fminimizer_set(s3, &F3, *nu, *nuLow, *nuUp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:647:15: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
nu_hi = gsl_root_fsolver_x_upper(s2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:348:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
x_hi = gsl_root_fsolver_x_upper(s);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function 'flowClustGaussian':
flowClustGaussian.c:207:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
x_hi = gsl_root_fsolver_x_upper(s);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ranMVNT.c -o ranMVNT.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o flowClust.dll tmp.def BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -L/i386/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/flowClust.buildbin-libdir/00LOCK-flowClust/00new/flowClust/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'Map' in package 'flowClust'
** help
*** installing help indices
converting help for package 'flowClust'
finding HTML links ... done
BIC html
Map html
SimulateMixture html
Subset html
box html
density html
dmvt html
dmvtmix html
flowClust-package html
flowClust html
flowClust.den html
flowClust2Prior html
hist html
miscellaneous html
mkPrior html
peakMatch html
plot.flowClust html
plot.flowCore html
plot.flowDens html
plotPrior html
rbox html
rituximab html
ruleOutliers html
show.flowClust html
split html
summary html
tmixFilter html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATYksx/R.INSTALL1c7835d32b27/flowClust/man/tmixFilter.Rd:63: file link 'filter' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATYksx/R.INSTALL1c7835d32b27/flowClust/man/tmixFilter.Rd:75: file link 'filter' in package 'flowCore' does not exist and so has been treated as a topic
** 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 'flowClust' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BoxCox.c -o BoxCox.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BoxCoxPriors.c -o BoxCoxPriors.o
BoxCoxPriors.c: In function 'BoxCoxGradientPriors':
BoxCoxPriors.c:57:16: warning: unused variable 'rowZ' [-Wunused-variable]
rowPrecision, rowZ, rowLambda0;
^~~~
BoxCoxPriors.c:33:24: warning: unused variable 'kappa0' [-Wunused-variable]
double *nu0 = p->nu0, kappa0 = p->kappa0;
^~~~~~
BoxCoxPriors.c:32:7: warning: unused variable 'itersolve' [-Wunused-variable]
int *itersolve = p->itersolve;
^~~~~~~~~
BoxCoxPriors.c:31:6: warning: unused variable 'iter' [-Wunused-variable]
int iter = p->iter;
^~~~
BoxCoxPriors.c:28:6: warning: unused variable 'model' [-Wunused-variable]
int model = *p->model;
^~~~~
BoxCoxPriors.c:23:14: warning: unused variable 'SumZlogY' [-Wunused-variable]
gsl_vector *SumZlogY = p->SumZlogY;
^~~~~~~~
BoxCoxPriors.c:15:14: warning: unused variable 'Precision' [-Wunused-variable]
gsl_matrix *Precision = p->Precision; // will be updated
^~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Nu.c -o Nu.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flowClust.c -o flowClust.o
flowClust.c: In function 'flowClust':
flowClust.c:48:2: warning: unused variable 'matrixZUY2' [-Wunused-variable]
matrixZUY2;
^~~~~~~~~~
flowClust.c:46:48: warning: unused variable 'subRowZUY2' [-Wunused-variable]
rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
^~~~~~~~~~
flowClust.c:46:39: warning: unused variable 'rowZUY2' [-Wunused-variable]
rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
^~~~~~~
flowClust.c: In function 'ECMUpdateSigmaG2':
flowClust.c:1111:6: warning: unused variable 'i' [-Wunused-variable]
int i=0;
^
At top level:
flowClust.c:10:27: warning: 'CEntries' defined but not used [-Wunused-const-variable=]
static const R_CMethodDef CEntries[] = { { "flowClust", (DL_FUNC) & flowClust,
^~~~~~~~
flowClust.c: In function 'flowClust':
flowClust.c:702:13: warning: 's3' may be used uninitialized in this function [-Wmaybe-uninitialized]
status = gsl_min_fminimizer_set(s3, &F3, *nu, *nuLow, *nuUp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:647:15: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
nu_hi = gsl_root_fsolver_x_upper(s2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:348:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
x_hi = gsl_root_fsolver_x_upper(s);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function 'flowClustGaussian':
flowClustGaussian.c:207:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
x_hi = gsl_root_fsolver_x_upper(s);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ranMVNT.c -o ranMVNT.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o flowClust.dll tmp.def BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -L/x64/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/flowClust.buildbin-libdir/flowClust/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowClust' as flowClust_3.28.0.zip
* DONE (flowClust)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'flowClust' successfully unpacked and MD5 sums checked