| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-02-27 02:34:43 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| 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 | ||||
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To the developers/maintainers of the SIMLR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIMLR.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. |
| Package 1873/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIMLR 1.25.1 (landing page) Luca De Sano
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: SIMLR |
| Version: 1.25.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SIMLR_1.25.1.tar.gz |
| StartedAt: 2023-02-24 18:39:20 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 18:57:43 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 1102.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIMLR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SIMLR_1.25.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SIMLR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.25.1’
* 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 ‘SIMLR’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 3.3Mb
libs 1.9Mb
* 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
SIMLR_Feature_Ranking 307.891 0.739 308.669
SIMLR 32.488 0.269 35.870
SIMLR_Estimate_Number_of_Clusters 4.654 0.070 7.950
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘vignette.Rnw’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SIMLR.Rcheck/00check.log’
for details.
SIMLR.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SIMLR
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘SIMLR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Rtsne.cpp -o Rtsne.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c package_init.c -o package_init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c projsplx_R.c -o projsplx_R.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c sptree.cpp -o sptree.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c tsne.cpp -o tsne.o
tsne.cpp: In member function ‘bool TSNE::load_data(double**, int*, int*, int*, double*, double*, int*)’:
tsne.cpp:979:48: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
979 | if (fread(*data, sizeof(double), *n * *d, h) != *n * *d) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
In file included from tsne.cpp:43:
vptree.h: In instantiation of ‘void VpTree<T, distance>::search(VpTree<T, distance>::Node*, const T&, int, std::priority_queue<VpTree<T, distance>::HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance; typename std::vector<VpTree<T, distance>::HeapItem, std::allocator<VpTree<T, distance>::HeapItem> >::value_type = VpTree<DataPoint, precomputed_distance>::HeapItem]’:
vptree.h:131:15: required from ‘void VpTree<T, distance>::search(const T&, int, std::vector<T>*, std::vector<double>*) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance]’
tsne.cpp:484:21: required from here
vptree.h:237:28: warning: comparison of integer expressions of different signedness: ‘std::priority_queue<VpTree<DataPoint, precomputed_distance>::HeapItem, std::vector<VpTree<DataPoint, precomputed_distance>::HeapItem, std::allocator<VpTree<DataPoint, precomputed_distance>::HeapItem> >, std::less<VpTree<DataPoint, precomputed_distance>::HeapItem> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
237 | if(heap.size() == k) heap.pop(); // remove furthest node from result list (if we already have k results)
| ~~~~~~~~~~~~^~~~
In file included from tsne.cpp:43:
vptree.h:239:28: warning: comparison of integer expressions of different signedness: ‘std::priority_queue<VpTree<DataPoint, precomputed_distance>::HeapItem, std::vector<VpTree<DataPoint, precomputed_distance>::HeapItem, std::allocator<VpTree<DataPoint, precomputed_distance>::HeapItem> >, std::less<VpTree<DataPoint, precomputed_distance>::HeapItem> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
239 | if(heap.size() == k) _tau = heap.top().dist; // update value of tau (farthest point in result list)
| ~~~~~~~~~~~~^~~~
In file included from tsne.cpp:43:
vptree.h: In instantiation of ‘void VpTree<T, distance>::search(VpTree<T, distance>::Node*, const T&, int, std::priority_queue<VpTree<T, distance>::HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance; typename std::vector<VpTree<T, distance>::HeapItem, std::allocator<VpTree<T, distance>::HeapItem> >::value_type = VpTree<DataPoint, euclidean_distance>::HeapItem]’:
vptree.h:131:15: required from ‘void VpTree<T, distance>::search(const T&, int, std::vector<T>*, std::vector<double>*) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance]’
tsne.cpp:562:21: required from here
vptree.h:237:28: warning: comparison of integer expressions of different signedness: ‘std::priority_queue<VpTree<DataPoint, euclidean_distance>::HeapItem, std::vector<VpTree<DataPoint, euclidean_distance>::HeapItem, std::allocator<VpTree<DataPoint, euclidean_distance>::HeapItem> >, std::less<VpTree<DataPoint, euclidean_distance>::HeapItem> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
237 | if(heap.size() == k) heap.pop(); // remove furthest node from result list (if we already have k results)
| ~~~~~~~~~~~~^~~~
In file included from tsne.cpp:43:
vptree.h:239:28: warning: comparison of integer expressions of different signedness: ‘std::priority_queue<VpTree<DataPoint, euclidean_distance>::HeapItem, std::vector<VpTree<DataPoint, euclidean_distance>::HeapItem, std::allocator<VpTree<DataPoint, euclidean_distance>::HeapItem> >, std::less<VpTree<DataPoint, euclidean_distance>::HeapItem> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
239 | if(heap.size() == k) _tau = heap.top().dist; // update value of tau (farthest point in result list)
| ~~~~~~~~~~~~^~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o SIMLR.so RcppExports.o Rtsne.o package_init.o projsplx_R.o sptree.o tsne.o -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-SIMLR/00new/SIMLR/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 (SIMLR)
SIMLR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv("R_TESTS" = "")
>
> library("testthat")
> library("SIMLR")
>
> test_check("SIMLR")
Computing the multiple Kernels.
Performing network diffiusion.
Iteration: 1
Iteration: 2
Iteration: 3
Iteration: 4
Iteration: 5
Iteration: 6
Iteration: 7
Iteration: 8
Iteration: 9
Iteration: 10
Iteration: 11
Performing t-SNE.
Epoch: Iteration # 100 error is: 0.116549
Epoch: Iteration # 200 error is: 0.06065268
Epoch: Iteration # 300 error is: 0.05890966
Epoch: Iteration # 400 error is: 0.0588568
Epoch: Iteration # 500 error is: 0.05880875
Epoch: Iteration # 600 error is: 0.0587633
Epoch: Iteration # 700 error is: 0.05872061
Epoch: Iteration # 800 error is: 0.05868041
Epoch: Iteration # 900 error is: 0.05864268
Epoch: Iteration # 1000 error is: 0.05860708
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.30844
Epoch: Iteration # 200 error is: 0.6306079
Epoch: Iteration # 300 error is: 0.4683815
Epoch: Iteration # 400 error is: 0.3232054
Epoch: Iteration # 500 error is: 0.2808782
Epoch: Iteration # 600 error is: 0.1475192
Epoch: Iteration # 700 error is: 0.1334575
Epoch: Iteration # 800 error is: 0.09764729
Epoch: Iteration # 900 error is: 0.0867104
Epoch: Iteration # 1000 error is: 0.08670834
Computing the multiple Kernels.
Performing network diffiusion.
Iteration: 1
Iteration: 2
Iteration: 3
Iteration: 4
Iteration: 5
Iteration: 6
Iteration: 7
Iteration: 8
Iteration: 9
Iteration: 10
Iteration: 11
Iteration: 12
Iteration: 13
Iteration: 14
Iteration: 15
Iteration: 16
Iteration: 17
Performing t-SNE.
Epoch: Iteration # 100 error is: 0.07855684
Epoch: Iteration # 200 error is: 0.07297176
Epoch: Iteration # 300 error is: 0.0661014
Epoch: Iteration # 400 error is: 0.06407188
Epoch: Iteration # 500 error is: 0.06383968
Epoch: Iteration # 600 error is: 0.06366181
Epoch: Iteration # 700 error is: 0.06351564
Epoch: Iteration # 800 error is: 0.06339399
Epoch: Iteration # 900 error is: 0.06329276
Epoch: Iteration # 1000 error is: 0.06320335
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.90323
Epoch: Iteration # 200 error is: 0.8004911
Epoch: Iteration # 300 error is: 0.510081
Epoch: Iteration # 400 error is: 0.5544615
Epoch: Iteration # 500 error is: 0.3654943
Epoch: Iteration # 600 error is: 0.2417727
Epoch: Iteration # 700 error is: 0.155308
Epoch: Iteration # 800 error is: 0.1534641
Epoch: Iteration # 900 error is: 0.1475339
Epoch: Iteration # 1000 error is: 0.146893
Computing the multiple Kernels.
Performing network diffiusion.
Iteration: 1
Iteration: 2
Iteration: 3
Iteration: 4
Iteration: 5
Iteration: 6
Iteration: 7
Iteration: 8
Iteration: 9
Iteration: 10
Iteration: 11
Performing t-SNE.
Epoch: Iteration # 100 error is: 0.1212328
Epoch: Iteration # 200 error is: 0.07207202
Epoch: Iteration # 300 error is: 0.05874404
Epoch: Iteration # 400 error is: 0.05861954
Epoch: Iteration # 500 error is: 0.0585089
Epoch: Iteration # 600 error is: 0.05841292
Epoch: Iteration # 700 error is: 0.0583249
Epoch: Iteration # 800 error is: 0.05824626
Epoch: Iteration # 900 error is: 0.05817584
Epoch: Iteration # 1000 error is: 0.05810977
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 10.52573
Epoch: Iteration # 200 error is: 0.5435558
Epoch: Iteration # 300 error is: 0.4034531
Epoch: Iteration # 400 error is: 0.6689465
Epoch: Iteration # 500 error is: 0.6157704
Epoch: Iteration # 600 error is: 0.4433442
Epoch: Iteration # 700 error is: 0.5105737
Epoch: Iteration # 800 error is: 0.4319828
Epoch: Iteration # 900 error is: 0.4244591
Epoch: Iteration # 1000 error is: 0.3265833
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[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
346.943 1.552 357.865
SIMLR.Rcheck/SIMLR-Ex.timings
| name | user | system | elapsed | |
| CIMLR | 0 | 0 | 0 | |
| CIMLR_Estimate_Number_of_Clusters | 0 | 0 | 0 | |
| SIMLR | 32.488 | 0.269 | 35.870 | |
| SIMLR_Estimate_Number_of_Clusters | 4.654 | 0.070 | 7.950 | |
| SIMLR_Feature_Ranking | 307.891 | 0.739 | 308.669 | |
| SIMLR_Large_Scale | 0.063 | 0.000 | 0.064 | |