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CHECK report for SIMLR on malbec2

This page was generated on 2019-10-16 12:09:41 -0400 (Wed, 16 Oct 2019).

Package 1527/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMLR 1.10.0
Luca De Sano
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/SIMLR
Branch: RELEASE_3_9
Last Commit: f4050a9
Last Changed Date: 2019-05-02 11:54:03 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SIMLR
Version: 1.10.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SIMLR_1.10.0.tar.gz
StartedAt: 2019-10-16 05:04:26 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:10:24 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 358.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: SIMLR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SIMLR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SIMLR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SIMLR’ can be installed ... WARNING
Found the following significant warnings:
  tsne.cpp:938:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  tsne.cpp:939:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  tsne.cpp:940:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  tsne.cpp:941:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  tsne.cpp:942:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  tsne.cpp:945:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  tsne.cpp:946:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/SIMLR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    libs   1.7Mb
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                    user system elapsed
SIMLR_Feature_Ranking             90.786  0.640  91.491
SIMLR                             20.908  0.312  24.126
SIMLR_Estimate_Number_of_Clusters  3.065  0.136   6.399
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/SIMLR.Rcheck/00check.log’
for details.

Installation output

SIMLR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SIMLR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘SIMLR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c Rtsne.cpp -o Rtsne.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c projsplx_R.c -o projsplx_R.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c sptree.cpp -o sptree.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c tsne.cpp -o tsne.o
In file included from tsne.cpp:41:0:
vptree.h: In instantiation of ‘void VpTree::search(VpTree::Node*, const T&, int, std::priority_queue::HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance; typename std::vector::HeapItem, std::allocator::HeapItem> >::value_type = VpTree::HeapItem]’:
vptree.h:131:15:   required from ‘void VpTree::search(const T&, int, std::vector*, std::vector*) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance]’
tsne.cpp:472:59:   required from here
vptree.h:237:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if(heap.size() == k) heap.pop();                 // remove furthest node from result list (if we already have k results)
In file included from tsne.cpp:41:0:
vptree.h:239:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if(heap.size() == k) _tau = heap.top().dist;     // update value of tau (farthest point in result list)
In file included from tsne.cpp:41:0:
vptree.h: In instantiation of ‘void VpTree::search(VpTree::Node*, const T&, int, std::priority_queue::HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance; typename std::vector::HeapItem, std::allocator::HeapItem> >::value_type = VpTree::HeapItem]’:
vptree.h:131:15:   required from ‘void VpTree::search(const T&, int, std::vector*, std::vector*) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance]’
tsne.cpp:550:59:   required from here
vptree.h:237:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if(heap.size() == k) heap.pop();                 // remove furthest node from result list (if we already have k results)
In file included from tsne.cpp:41:0:
vptree.h:239:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if(heap.size() == k) _tau = heap.top().dist;     // update value of tau (farthest point in result list)
tsne.cpp: In member function ‘bool TSNE::load_data(double**, int*, int*, int*, double*, double*, int*)’:
tsne.cpp:938:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  fread(n, sizeof(int), 1, h);           // number of datapoints
  ~~~~~^~~~~~~~~~~~~~~~~~~~~~
tsne.cpp:939:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  fread(d, sizeof(int), 1, h);           // original dimensionality
  ~~~~~^~~~~~~~~~~~~~~~~~~~~~
tsne.cpp:940:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
     fread(theta, sizeof(double), 1, h);          // gradient accuracy
     ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tsne.cpp:941:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  fread(perplexity, sizeof(double), 1, h);        // perplexity
  ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tsne.cpp:942:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fread(no_dims, sizeof(int), 1, h);                                      // output dimensionality
   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
tsne.cpp:945:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
     fread(*data, sizeof(double), *n * *d, h);                               // the data
     ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tsne.cpp:946:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  if(!feof(h)) fread(rand_seed, sizeof(int), 1, h);                       // random seed
               ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o SIMLR.so RcppExports.o Rtsne.o projsplx_R.o sptree.o tsne.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-SIMLR/00new/SIMLR/libs
** R
** data
*** moving datasets to lazyload DB
** 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)

Tests output

SIMLR.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-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:  0.1326426 
Epoch: Iteration # 200  error is:  0.08721104 
Epoch: Iteration # 300  error is:  0.05808032 
Epoch: Iteration # 400  error is:  0.05713627 
Epoch: Iteration # 500  error is:  0.0570977 
Epoch: Iteration # 600  error is:  0.0570602 
Epoch: Iteration # 700  error is:  0.05702496 
Epoch: Iteration # 800  error is:  0.05699161 
Epoch: Iteration # 900  error is:  0.05696026 
Epoch: Iteration # 1000  error is:  0.05693017 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.82289 
Epoch: Iteration # 200  error is:  1.18051 
Epoch: Iteration # 300  error is:  0.5294717 
Epoch: Iteration # 400  error is:  0.4658907 
Epoch: Iteration # 500  error is:  0.3601786 
Epoch: Iteration # 600  error is:  0.4378043 
Epoch: Iteration # 700  error is:  0.3978081 
Epoch: Iteration # 800  error is:  0.4071172 
Epoch: Iteration # 900  error is:  0.3122373 
Epoch: Iteration # 1000  error is:  0.302183 
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:  0.07916304 
Epoch: Iteration # 200  error is:  0.07265125 
Epoch: Iteration # 300  error is:  0.06588937 
Epoch: Iteration # 400  error is:  0.06431247 
Epoch: Iteration # 500  error is:  0.06408182 
Epoch: Iteration # 600  error is:  0.06389943 
Epoch: Iteration # 700  error is:  0.06375158 
Epoch: Iteration # 800  error is:  0.06362855 
Epoch: Iteration # 900  error is:  0.06352469 
Epoch: Iteration # 1000  error is:  0.06343539 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.29436 
Epoch: Iteration # 200  error is:  0.9751335 
Epoch: Iteration # 300  error is:  0.5030286 
Epoch: Iteration # 400  error is:  0.2498062 
Epoch: Iteration # 500  error is:  0.1590792 
Epoch: Iteration # 600  error is:  0.1568111 
Epoch: Iteration # 700  error is:  0.1554006 
Epoch: Iteration # 800  error is:  0.1540344 
Epoch: Iteration # 900  error is:  0.1522608 
Epoch: Iteration # 1000  error is:  0.1502272 
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:  0.1188644 
Epoch: Iteration # 200  error is:  0.06789612 
Epoch: Iteration # 300  error is:  0.05787332 
Epoch: Iteration # 400  error is:  0.05782322 
Epoch: Iteration # 500  error is:  0.05777752 
Epoch: Iteration # 600  error is:  0.05773384 
Epoch: Iteration # 700  error is:  0.05769336 
Epoch: Iteration # 800  error is:  0.05765563 
Epoch: Iteration # 900  error is:  0.05761978 
Epoch: Iteration # 1000  error is:  0.0575862 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.09871 
Epoch: Iteration # 200  error is:  0.4317859 
Epoch: Iteration # 300  error is:  0.1544812 
Epoch: Iteration # 400  error is:  0.1348888 
Epoch: Iteration # 500  error is:  0.09253927 
Epoch: Iteration # 600  error is:  0.08800723 
Epoch: Iteration # 700  error is:  0.08796193 
Epoch: Iteration # 800  error is:  0.08793287 
Epoch: Iteration # 900  error is:  0.08789588 
Epoch: Iteration # 1000  error is:  0.08787819 
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══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 4 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
160.059   1.168 169.406

Example timings

SIMLR.Rcheck/SIMLR-Ex.timings

nameusersystemelapsed
SIMLR20.908 0.31224.126
SIMLR_Estimate_Number_of_Clusters3.0650.1366.399
SIMLR_Feature_Ranking90.786 0.64091.491
SIMLR_Large_Scale0.0540.0000.054