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CHECK report for dada2 on malbec2

This page was generated on 2019-10-16 12:08:22 -0400 (Wed, 16 Oct 2019).

Package 384/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.12.1
Benjamin Callahan
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/dada2
Branch: RELEASE_3_9
Last Commit: f4423b9
Last Changed Date: 2019-05-07 18:03:04 -0400 (Tue, 07 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  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: dada2
Version: 1.12.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:dada2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings dada2_1.12.1.tar.gz
StartedAt: 2019-10-16 00:56:34 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:01:13 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 279.3 seconds
RetCode: 0
Status:  OK 
CheckDir: dada2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:dada2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings dada2_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/dada2.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 ‘dada2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dada2’ version ‘1.12.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dada2’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    extdata   1.2Mb
    libs      6.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘ShortRead:::.set_omp_threads’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
plotComplexity: no visible binding for global variable ‘complexity’
plotErrors: no visible binding for global variable ‘Qual’
plotErrors: no visible binding for global variable ‘Observed’
plotErrors: no visible binding for global variable ‘Input’
plotErrors: no visible binding for global variable ‘Estimated’
plotErrors: no visible binding for global variable ‘Nominal’
plotQualityProfile: no visible binding for global variable ‘Cycle’
plotQualityProfile: no visible binding for global variable ‘Score’
plotQualityProfile: no visible binding for global variable ‘Count’
plotQualityProfile: no visible binding for global variable ‘Mean’
plotQualityProfile: no visible binding for global variable ‘Q25’
plotQualityProfile: no visible binding for global variable ‘Q50’
plotQualityProfile: no visible binding for global variable ‘Q75’
plotQualityProfile: no visible binding for global variable ‘Cum’
seqtab_to_mothur: no visible binding for global variable ‘four’
Undefined global functions or variables:
  Count Cum Cycle Estimated Input Mean Nominal Observed Q25 Q50 Q75
  Qual Score complexity four
* 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 ... NOTE
GNU make is a SystemRequirements.
* 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
PacBioErrfun 12.033  0.028  12.103
learnErrors   9.203  0.139   7.952
* 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: 8 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/dada2.Rcheck/00check.log’
for details.

Installation output

dada2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL dada2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘dada2’ ...
** 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"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/dada2.h:7:0,
                 from RcppExports.cpp:4:
../inst/include/dada2_RcppExports.h:14:14: warning: ‘void dada2::{anonymous}::validateSignature(const char*)’ defined but not used [-Wunused-function]
         void validateSignature(const char* sig) {
              ^~~~~~~~~~~~~~~~~
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"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function ‘Rcpp::List dada_uniques(std::vector >, std::vector, std::vector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)’:
Rmain.cpp:68:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(quals.nrow() != maxlen) {
        ~~~~~~~~~~~~~^~~~~~~~~
Rmain.cpp:81:8: warning: variable ‘HW_SSE3’ set but not used [-Wunused-but-set-variable]
   bool HW_SSE3 = false;
        ^~~~~~~
Rmain.cpp: In function ‘B* run_dada(Raw**, int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, double, double, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)’:
Rmain.cpp:307:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, min_abund, verbose)) ) {
           ~~~~~~~~~~~^~~~~~~~~~~
Rmain.cpp: In function ‘Rcpp::List dada_uniques(std::vector >, std::vector, std::vector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)’:
Rmain.cpp:282:9: warning: ‘kord’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(kord);
     ~~~~^~~~~~
Rmain.cpp:281:9: warning: ‘k16’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k16);
     ~~~~^~~~~
Rmain.cpp:280:9: warning: ‘k8’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k8);
     ~~~~^~~~
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"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chimera.cpp -o chimera.o
chimera.cpp: In function ‘bool C_is_bimera(std::__cxx11::string, std::vector >, bool, int, int, int, int, int)’:
chimera.cpp:25:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
        ~~~~~~~~~~~~~^~~~~~~~~~~~
chimera.cpp:44:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if((max_right+max_left)>=sq.size()) {
        ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp:48:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp:48:83: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
                                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp: In function ‘void get_lr(char**, int&, int&, int&, int&, bool, int)’:
chimera.cpp:231:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(al[0][pos] == '-' && pos+(len-max_shift)) {
                              ~~~^~~~~~~~~~~~~~~~~
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"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c cluster.cpp -o cluster.o
cluster.cpp: In function ‘void b_compare(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)’:
cluster.cpp:17:23: warning: variable ‘cind’ set but not used [-Wunused-but-set-variable]
   unsigned int index, cind, center_reads;
                       ^~~~
cluster.cpp: In function ‘void b_compare_parallel(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)’:
cluster.cpp:166:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(row=0;rownclust;i++) {
           ~^~~~~~~~~~
cluster.cpp:318:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(r=1; rbi[i]->nraw; r++) { // r=0 is the center
              ~^~~~~~~~~~~~~~~
cluster.cpp:321:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(raw->reads < min_abund) { continue; }
          ~~~~~~~~~~~^~~~~~~~~~~
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"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c containers.cpp -o containers.o
containers.cpp: In function ‘void b_free(B*)’:
containers.cpp:140:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;inclust;i++) { bi_free(b->bi[i]); }
               ~^~~~~~~~~~
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"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c error.cpp -o error.o
error.cpp: In function ‘Rcpp::DataFrame b_make_positional_substitution_df(B*, Sub**, unsigned int, Rcpp::NumericMatrix, bool)’:
error.cpp:170:51: warning: variable ‘ncol’ set but not used [-Wunused-but-set-variable]
   unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
                                                   ^~~~
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"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function ‘Rcpp::IntegerVector C_eval_pair(std::__cxx11::string, std::__cxx11::string)’:
evaluate.cpp:88:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   } while((s1gap || s2gap) && start >, std::vector >, int)’:
evaluate.cpp:219:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i >, std::vector >, int, int)’:
evaluate.cpp:243:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i >, std::vector >, int)’:
evaluate.cpp:286:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i >, std::vector >, int)’:
evaluate.cpp:339:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i >, std::__cxx11::string, unsigned int, bool)’:
filter.cpp:16:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ~~^~~~~~
kmers.cpp:158:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0; i= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ~~^~~~~~
kmers.cpp:205:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0; i= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ~~^~~~~~
kmers.cpp:239:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i=0 && (band=0 && (bandlen2) { r = len2; }
                       ~^~~~~
nwalign_endsfree.cpp:130:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
           ~~^~~~~~~
nwalign_endsfree.cpp:137:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
           ~~^~~~~~~
nwalign_endsfree.cpp:201:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0;i=0 && (band=0 && (bandlen2) { r = len2; }
                       ~^~~~~
nwalign_endsfree.cpp:305:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
           ~~^~~~~~~
nwalign_endsfree.cpp:314:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
           ~~^~~~~~~
nwalign_endsfree.cpp:379:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0;i=0 && (band=0 && (bandlen2) { r = len2; }
                       ~^~~~~
nwalign_endsfree.cpp:522:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0;insubs;s++) {
               ~^~~~~~~~~~~
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"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function ‘char** nwalign_vectorized2(const char*, size_t, const char*, size_t, int16_t, int16_t, int16_t, int16_t, int)’:
nwalign_vectorized.cpp:96:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   start_col = 1 + (1+(band >, std::vector >, int16_t, int16_t, int16_t, int, bool)’:
nwalign_vectorized.cpp:330:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;insubs;s++) {
           ~^~~~~~~~~~~
pval.cpp:123:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
                    ~~~~~^~~~~~~~~~~~
pval.cpp: In function ‘double compute_lambda_ts(Raw*, Sub*, unsigned int, double*, bool)’:
pval.cpp:177:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(s=0;snsubs;s++) {
           ~^~~~~~~~~~~
pval.cpp:179:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
                    ~~~~~^~~~~~~~~~~~
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"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function ‘void tax_kvec(const char*, unsigned int, unsigned char*)’:
taxonomy.cpp:42:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(kmer>=0 && kmer >, std::vector >, std::vector >, std::vector, Rcpp::IntegerMatrix, bool, bool)’:
taxonomy.cpp:120:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
taxonomy.cpp:149:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(kmer=0;kmer >, std::vector >, std::vector >, std::vector, Rcpp::IntegerMatrix, bool, bool)’:
taxonomy.cpp:345:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
taxonomy.cpp:374:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(kmer=0;kmer

Tests output

Example timings

dada2.Rcheck/dada2-Ex.timings

nameusersystemelapsed
PacBioErrfun12.033 0.02812.103
addSpecies2.2230.0242.538
assignSpecies0.6830.0000.682
assignTaxonomy0.2250.0120.235
collapseNoMismatch1.0850.0001.104
dada4.7310.0244.784
derepFastq0.7430.0000.743
fastqFilter0.6950.0000.696
fastqPairedFilter1.1390.0081.151
filterAndTrim1.2480.0041.259
getDadaOpt0.0010.0000.001
getErrors1.8630.0041.876
getSequences0.5630.0080.573
getUniques0.4770.0040.481
inflateErr0.0010.0000.000
isBimera0.0650.0080.074
isBimeraDenovo3.2140.0123.238
isBimeraDenovoTable4.9120.0164.940
isPhiX0.2720.0040.280
isShiftDenovo1.8710.0041.879
learnErrors9.2030.1397.952
loessErrfun0.5400.0000.541
makeSequenceTable1.0130.0041.021
mergePairs4.0080.0124.036
mergeSequenceTables000
noqualErrfun1.3490.0001.351
nwalign0.0000.0000.001
nwhamming0.0010.0000.001
plotComplexity0.3650.0000.367
plotErrors2.5860.0712.672
plotQualityProfile2.5520.4653.131
rc0.0260.0000.027
removeBimeraDenovo3.3200.0123.333
removePrimers0.2870.0000.297
seqComplexity0.0320.0000.035
setDadaOpt0.0010.0000.001
uniquesToFasta0.7270.0040.731