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This page was generated on 2023-04-12 10:55:42 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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INSTALL results for SIMLR on nebbiolo2


To the developers/maintainers of the SIMLR package:
- 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 Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1907/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMLR 1.25.4  (landing page)
Luca De Sano
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/SIMLR
git_branch: devel
git_last_commit: 80a8f7f
git_last_commit_date: 2023-04-06 03:43:23 -0400 (Thu, 06 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: SIMLR
Version: 1.25.4
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SIMLR
StartedAt: 2023-04-12 01:34:39 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 01:35:18 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 38.5 seconds
RetCode: 0
Status:   OK  

Command output

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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/site-library’
* installing *source* package ‘SIMLR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-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/site-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/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c projsplx_R.c -o projsplx_R.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c sptree.cpp -o sptree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-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:131:9:   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:484:59:   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:131:9:   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:562:59:   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++17 -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 -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-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)