| Back to Long tests report for BioC 3.8 |
This page was generated on 2019-04-13 19:55:02 -0400 (Sat, 13 Apr 2019).
| Package 1/4 | Hostname | OS / Arch | CHECK | |||||
| beachmat 1.4.0 Aaron Lun
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | [ OK ] |
| Package: beachmat |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no beachmat_1.4.0.tar.gz |
| StartedAt: 2019-04-13 11:55:21 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 12:27:50 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 1948.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: beachmat.Rcheck |
| Warnings: 0 |
beachmat.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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.
> library(testthat)
> library(beachmat)
> test_check("beachmat")
── Building ─────────────────────────────────────────────────────── beachtest ──
Setting env vars:
● CFLAGS : -Wall -pedantic
● CXXFLAGS : -Wall -pedantic
● CXX11FLAGS: -Wall -pedantic
────────────────────────────────────────────────────────────────────────────────
checking for file ‘/home/biocbuild/bbs-3.8-bioc-longtests/meat/beachmat.Rcheck/beachmat/testpkg/DESCRIPTION’ ...
✔ checking for file ‘/home/biocbuild/bbs-3.8-bioc-longtests/meat/beachmat.Rcheck/beachmat/testpkg/DESCRIPTION’
─ preparing ‘beachtest’:
checking DESCRIPTION meta-information ...
✔ checking DESCRIPTION meta-information
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘beachtest_1.0.0.tar.gz’
── Checking ─────────────────────────────────────────────────────── beachtest ──
Setting env vars:
● _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
● _R_CHECK_CRAN_INCOMING_ : FALSE
● _R_CHECK_FORCE_SUGGESTS_ : FALSE
── R CMD check ─────────────────────────────────────────────────────────────────
─ using log directory ‘/tmp/RtmpCOYnAj/beachtest.Rcheck’
─ using R version 3.5.3 (2019-03-11)
─ using platform: x86_64-pc-linux-gnu (64-bit)
─ using session charset: UTF-8
─ using options ‘--no-manual --as-cran’
✔ checking for file ‘beachtest/DESCRIPTION’
─ this is package ‘beachtest’ version ‘1.0.0’
checking package namespace information ...
✔ checking package namespace information
checking package dependencies ...
─ checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: (6m 22.5s)
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
checking if this is a source package ...
✔ checking if this is a source package
✔ checking if there is a namespace
✔ checking for hidden files and directories
checking for portable file names ...
✔ checking for portable file names
✔ checking for sufficient/correct file permissions
✔ checking serialization versions
checking whether package ‘beachtest’ can be installed ...
✔ checking whether package ‘beachtest’ can be installed (1m 16.1s)
checking installed package size ...
N checking installed package size
installed size is 9.7Mb
sub-directories of 1Mb or more:
libs 9.6Mb
checking package directory ...
✔ checking package directory
checking DESCRIPTION meta-information ...
✔ checking DESCRIPTION meta-information
✔ checking top-level files
✔ checking for left-over files
✔ checking index information
checking package subdirectories ...
✔ checking package subdirectories
checking R files for non-ASCII characters ...
✔ checking R files for non-ASCII characters
checking R files for syntax errors ...
✔ checking R files for syntax errors
checking whether the package can be loaded ...
✔ checking whether the package can be loaded (2.3s)
checking whether the package can be loaded with stated dependencies ...
✔ checking whether the package can be loaded with stated dependencies (2.1s)
checking whether the package can be unloaded cleanly ...
✔ checking whether the package can be unloaded cleanly (2.1s)
checking whether the namespace can be loaded with stated dependencies ...
✔ checking whether the namespace can be loaded with stated dependencies (2.1s)
checking whether the namespace can be unloaded cleanly ...
✔ checking whether the namespace can be unloaded cleanly (2.2s)
checking loading without being on the library search path ...
✔ checking loading without being on the library search path (2.3s)
checking dependencies in R code ...
✔ checking dependencies in R code (2.1s)
checking S3 generic/method consistency ...
✔ checking S3 generic/method consistency (2.4s)
checking replacement functions ...
✔ checking replacement functions (2.1s)
checking foreign function calls ...
N checking foreign function calls (2.1s)
Registration problems:
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, ro, co, PACKAGE = "beachtest")
Evaluating ‘paste0("get_class_", mode)’ during check gives error
‘cannot coerce type 'closure' to vector of type 'character'’:
.Call(paste0("get_class_", mode), test.mat, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, b, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, b, PACKAGE = "beachtest")
Evaluating ‘paste0("get_row_", mode, "_to_", alt.mode)’ during check gives error
‘object 'alt.mode' not found’:
.Call(paste0("get_row_", mode, "_to_", alt.mode), test.mat, ordering,
PACKAGE = "beachtest")
Evaluating ‘paste0("get_col_", mode, "_to_", alt.mode)’ during check gives error
‘object 'alt.mode'
‘object 'alt.mode' not found’:
.Call(paste0("get_col_", mode, "_to_", alt.mode), test.mat, ordering,
PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, rbounds, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, cbounds, PACKAGE = "beachtest")
Evaluating ‘paste0("set_col_all_", mode)’ during check gives error
‘cannot coerce type 'closure' to vector of type 'character'’:
.Call(paste0("set_col_all_", mode), mats[[i]], seq_len(ncol(mats[[i]])))
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, ro, co, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, subr)
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, subr)
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating ‘paste0("set_row_", mode, "_via_", alt.mode)’ during check gives error
‘object 'alt.mode' not found’:
.Call(paste0("set_row_", mode, "_via_", alt.mode), test.mat,
ordering, PACKAGE = "beachtest")
Evaluating ‘paste0("set_col_", mode,
Evaluating ‘paste0("set_col_", mode, "_via_", alt.mode)’ during check gives error
‘object 'alt.mode' not found’:
.Call(paste0("set_col_", mode, "_via_", alt.mode), test.mat,
ordering, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, rbounds, PACKAGE = "beachtest")
Evaluating ‘paste0(FUN, "_", mode)’ during check gives error
‘object 'FUN' not found’:
.Call(paste0(FUN, "_", mode), test.mat, o, cbounds, PACKAGE = "beachtest")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
checking R code for possible problems ...
✔ checking R code for possible problems (8.5s)
checking for missing documentation entries ...
W checking for missing documentation entries (2s)
Undocumented code objects:
‘check_read_all’ ‘check_read_class’ ‘check_read_const’
‘check_read_errors’ ‘check_read_indexed’ ‘check_read_multi’
‘check_read_slice’ ‘check_read_type’ ‘check_read_varslice’
‘check_write_HDF5’ ‘check_write_all’ ‘check_write_class’
‘check_write_errors’ ‘check_write_indexed’ ‘check_write_slice’
‘check_write_type’ ‘check_write_varslice’ ‘delayed_funs’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking line endings in C/C++/Fortran sources/headers ...
✔ checking line endings in C/C++/Fortran sources/headers
checking line endings in Makefiles ...
✔ checking line endings in Makefiles
checking compilation flags in Makevars ...
✔ checking compilation flags in Makevars
✔ checking for GNU extensions in Makefiles
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ...
✔ checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS)
checking pragmas in C/C++ headers and code ...
✔ checking pragmas in C/C++ headers and code
✔ checking compilation flags used
checking compiled code ...
N checking compiled code
File ‘beachtest/libs/beachtest.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checking examples ...
─ checking examples ... NONE
checking for unstated dependencies in ‘tests’ ...
✔ checking for unstated dependencies in ‘tests’
checking tests ...
─ checking tests ...
Running ‘testthat.R’
✔ Running ‘testthat.R’ [468s/468s]
See
‘/tmp/RtmpCOYnAj/beachtest.Rcheck/00check.log’
for details.
── Building ─────────────────────────────────────────────────────── morebeach ──
Setting env vars:
● CFLAGS : -Wall -pedantic
● CXXFLAGS : -Wall -pedantic
● CXX11FLAGS: -Wall -pedantic
────────────────────────────────────────────────────────────────────────────────
checking for file ‘/home/biocbuild/bbs-3.8-bioc-longtests/meat/beachmat.Rcheck/beachmat/extensions/DESCRIPTION’ ...
✔ checking for file ‘/home/biocbuild/bbs-3.8-bioc-longtests/meat/beachmat.Rcheck/beachmat/extensions/DESCRIPTION’
─ preparing ‘morebeach’:
checking DESCRIPTION meta-information ...
✔ checking DESCRIPTION meta-information
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘morebeach_1.0.0.tar.gz’
── Checking ─────────────────────────────────────────────────────── morebeach ──
Setting env vars:
● _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
● _R_CHECK_CRAN_INCOMING_ : FALSE
● _R_CHECK_FORCE_SUGGESTS_ : FALSE
── R CMD check ─────────────────────────────────────────────────────────────────
─ using log directory ‘/tmp/RtmpCOYnAj/morebeach.Rcheck’
─ using R version 3.5.3 (2019-03-11)
─ using platform: x86_64-pc-linux-gnu (64-bit)
─ using session charset: UTF-8
─ using options ‘--no-manual --as-cran’
✔ checking for file ‘morebeach/DESCRIPTION’
─ this is package ‘morebeach’ version ‘1.0.0’
checking package namespace information ...
✔ checking package namespace information
checking package dependencies ...
─ checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: (6m 22.4s)
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
✔ checking if this is a source package
✔ checking if there is a namespace
✔ checking for hidden files and directories
✔ checking for portable file names
✔ checking for sufficient/correct file permissions
✔ checking serialization versions
checking whether package ‘morebeach’ can be installed ...
✔ checking whether package ‘morebeach’ can be installed (14.2s)
checking installed package size ...
✔ checking installed package size
checking package directory ...
✔ checking package directory
checking DESCRIPTION meta-information ...
✔ checking DESCRIPTION meta-information
checking top-level files ...
✔ checking top-level files
✔ checking for left-over files
✔ checking index information
checking package subdirectories ...
✔ checking package subdirectories
checking R files for non-ASCII characters ...
✔ checking R files for non-ASCII characters
checking R files for syntax errors ...
✔ checking R files for syntax errors
checking whether the package can be loaded ...
✔ checking whether the package can be loaded (2.1s)
checking whether the package can be loaded with stated dependencies ...
✔ checking whether the package can be loaded with stated dependencies (1.7s)
checking whether the package can be unloaded cleanly ...
✔ checking whether the package can be unloaded cleanly (1.7s)
checking whether the namespace can be loaded with stated dependencies ...
✔ checking whether the namespace can be loaded with stated dependencies (1.7s)
checking whether the namespace can be unloaded cleanly ...
✔ checking whether the namespace can be unloaded cleanly (1.9s)
checking loading without being on the library search path ...
✔ checking loading without being on the library search path (1.9s)
checking dependencies in R code ...
✔ checking dependencies in R code (1.7s)
checking S3 generic/method consistency ...
W checking S3 generic/method consistency (2.2s)
as.matrix:
function(x, ...)
as.matrix.AaronMatrix:
function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
as.matrix.AaronMatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
checking replacement functions ...
✔ checking replacement functions (1.8s)
checking foreign function calls ...
✔ checking foreign function calls (1.8s)
checking R code for possible problems ...
✔ checking R code for possible problems (6.4s)
checking for missing documentation entries ...
W checking for missing documentation entries (1.8s)
Undocumented code objects:
‘AaronMatrix’ ‘as.matrix.AaronMatrix’
Undocumented S4 classes:
‘AaronMatrix’
Undocumented S4 methods:
generic '[' and siglist 'AaronMatrix'
generic 'as.matrix' and siglist 'AaronMatrix'
generic 'dim' and siglist 'AaronMatrix'
generic 'supportCppAccess' and siglist 'AaronMatrix'
generic 'type' and siglist 'AaronMatrix'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
✔ checking line endings in C/C++/Fortran sources/headers
checking pragmas in C/C++ headers and code ...
✔ checking pragmas in C/C++ headers and code
✔ checking compilation flags used
checking compiled code ...
N checking compiled code
File ‘morebeach/libs/morebeach.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checking examples ...
─ checking examples ... NONE
checking for unstated dependencies in ‘tests’ ...
W checking for unstated dependencies in ‘tests’
'library' or 'require' call not declared from: ‘testthat’
checking tests ...
─ checking tests ...
Running ‘testthat.R’
✔ Running ‘testthat.R’ [77s/78s]
See
‘/tmp/RtmpCOYnAj/morebeach.Rcheck/00check.log’
for details.
══ testthat results ═══════════════════════════════════════════════════════════
OK: 2 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
688.976 16.460 1469.355
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no beachmat_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.8-bioc-longtests/meat/beachmat.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘beachmat/DESCRIPTION’ ... OK
* this is package ‘beachmat’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ‘beachmat’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 69.6Mb
sub-directories of 1Mb or more:
lib 44.4Mb
libs 24.4Mb
* checking package 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 ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘testthat.R’
OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.8-bioc-longtests/meat/beachmat.Rcheck/00check.log’
for details.
beachmat.Rcheck/00install.out
* installing *source* package ‘beachmat’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c HDF5_utils.cpp -o HDF5_utils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c character_matrix.cpp -o character_matrix.o
character_matrix.cpp: In member function ‘virtual beachmat::const_col_indexed_info<Rcpp::Vector<16> > beachmat::character_matrix::get_const_col_indexed(size_t, Rcpp::Vector<16>::iterator, size_t, size_t)’:
character_matrix.cpp:43:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
In file included from all_readers.h:8:0,
from character_matrix.h:4,
from character_matrix.cpp:1:
simple_reader.h: In instantiation of ‘beachmat::simple_reader<T, V>::simple_reader(const RObject&) [with T = Rcpp::String; V = Rcpp::Vector<16>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
character_matrix.h:60:78: required from ‘beachmat::general_character_matrix<RDR>::general_character_matrix(const RObject&) [with RDR = beachmat::simple_reader<Rcpp::String, Rcpp::Vector<16> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
character_matrix.cpp:52:119: required from here
simple_reader.h:59:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
In file included from all_readers.h:12:0,
from character_matrix.h:4,
from character_matrix.cpp:1:
delayed_reader.h: In instantiation of ‘static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long unsigned int>&) [with T = Rcpp::String; V = Rcpp::Vector<16>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
delayed_reader.h:115:19: required from ‘beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::character_matrix*; T = Rcpp::String; V = Rcpp::Vector<16>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]’
delayed_reader.h:371:20: required from ‘beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = Rcpp::String; V = Rcpp::Vector<16>; base_mat = beachmat::character_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
character_matrix.h:60:78: required from ‘beachmat::general_character_matrix<RDR>::general_character_matrix(const RObject&) [with RDR = beachmat::delayed_matrix<Rcpp::String, Rcpp::Vector<16>, beachmat::character_matrix>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
character_matrix.cpp:165:91: required from here
delayed_reader.h:154:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 1 || i > original_dim) {
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c character_output.cpp -o character_output.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c dim_checker.cpp -o dim_checker.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c find_chunks.cpp -o find_chunks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c functions.cpp -o functions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c integer_matrix.cpp -o integer_matrix.o
In file included from all_readers.h:8:0,
from LIN_matrix.h:4,
from integer_matrix.h:4,
from integer_matrix.cpp:1:
simple_reader.h: In instantiation of ‘beachmat::simple_reader<T, V>::simple_reader(const RObject&) [with T = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99: required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; RDR = beachmat::simple_reader<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:181:100: required from ‘beachmat::simple_lin_matrix<T, V>::simple_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integer_matrix.cpp:49:78: required from here
simple_reader.h:59:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
In file included from all_readers.h:12:0,
from LIN_matrix.h:4,
from integer_matrix.h:4,
from integer_matrix.cpp:1:
delayed_reader.h: In instantiation of ‘static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long unsigned int>&) [with T = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
delayed_reader.h:115:19: required from ‘beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; T = int; V = Rcpp::Vector<13>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]’
delayed_reader.h:371:20: required from ‘beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; base_mat = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:92:99: required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; RDR = beachmat::delayed_matrix<int, Rcpp::Vector<13>, beachmat::lin_matrix<int, Rcpp::Vector<13> > >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integer_matrix.cpp:43:87: required from here
delayed_reader.h:154:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 1 || i > original_dim) {
^
In file included from LIN_matrix.h:238:0,
from integer_matrix.h:4,
from integer_matrix.cpp:1:
LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
integer_matrix.cpp:70:1: required from here
LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c logical_matrix.cpp -o logical_matrix.o
In file included from all_readers.h:9:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
dense_reader.h: In instantiation of ‘beachmat::dense_reader<T, V>::dense_reader(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99: required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::dense_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:196:97: required from ‘beachmat::dense_lin_matrix<T, V>::dense_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
logical_matrix.cpp:51:85: required from here
dense_reader.h:60:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (x.size()!=(this->nrow)*NC) {
^
In file included from all_readers.h:10:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
Csparse_reader.h: In instantiation of ‘beachmat::Csparse_reader<T, V>::Csparse_reader(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99: required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:211:103: required from ‘beachmat::Csparse_lin_matrix<T, V>::Csparse_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
logical_matrix.cpp:53:87: required from here
Csparse_reader.h:78:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (NC+1!=p.size()) { throw_custom_error("length of 'p' slot in a ", ctype, " object should be equal to 'ncol+1'"); }
^
Csparse_reader.h:106:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curi<0 || curi>=NR) {
^
In file included from all_readers.h:8:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
simple_reader.h: In instantiation of ‘beachmat::simple_reader<T, V>::simple_reader(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99: required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::simple_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:181:100: required from ‘beachmat::simple_lin_matrix<T, V>::simple_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
logical_matrix.cpp:63:78: required from here
simple_reader.h:59:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
In file included from all_readers.h:12:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
delayed_reader.h: In instantiation of ‘static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long unsigned int>&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
delayed_reader.h:115:19: required from ‘beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::lin_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]’
delayed_reader.h:371:20: required from ‘beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; base_mat = beachmat::lin_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:92:99: required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::delayed_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage>, beachmat::lin_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> > >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
logical_matrix.cpp:57:87: required from here
delayed_reader.h:154:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 1 || i > original_dim) {
^
In file included from LIN_matrix.h:238:0,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
logical_matrix.cpp:86:1: required from here
LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
In file included from all_readers.h:10:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
LIN_methods_read.h:120:5: required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’
logical_matrix.cpp:86:1: required from here
Csparse_reader.h:208:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (idex!=*pIt && i[idex]==r) { (*out)=x[idex]; }
^
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = double*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
LIN_methods_read.h:126:5: required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]’
logical_matrix.cpp:86:1: required from here
Csparse_reader.h:208:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_reader.h: In instantiation of ‘T beachmat::Csparse_reader<T, V>::get(size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
LIN_methods_read.h:132:27: required from ‘T beachmat::general_lin_matrix<T, V, RDR>::get(size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long unsigned int]’
logical_matrix.cpp:86:1: required from here
Csparse_reader.h:121:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (loc!=iend && *loc==r) {
^
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<T, V>::update_indices(size_t, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
Csparse_reader.h:202:19: required from ‘void beachmat::Csparse_reader<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long unsigned int]’
LIN_methods_read.h:120:5: required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’
logical_matrix.cpp:86:1: required from here
Csparse_reader.h:164:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex] < r) {
^
Csparse_reader.h:171:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex-1] >= r) {
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c numeric_matrix.cpp -o numeric_matrix.o
In file included from all_readers.h:9:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
dense_reader.h: In instantiation of ‘beachmat::dense_reader<T, V>::dense_reader(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99: required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::dense_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:196:97: required from ‘beachmat::dense_lin_matrix<T, V>::dense_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
numeric_matrix.cpp:51:85: required from here
dense_reader.h:60:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (x.size()!=(this->nrow)*NC) {
^
In file included from all_readers.h:10:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
Csparse_reader.h: In instantiation of ‘beachmat::Csparse_reader<T, V>::Csparse_reader(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99: required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:211:103: required from ‘beachmat::Csparse_lin_matrix<T, V>::Csparse_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
numeric_matrix.cpp:53:87: required from here
Csparse_reader.h:78:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (NC+1!=p.size()) { throw_custom_error("length of 'p' slot in a ", ctype, " object should be equal to 'ncol+1'"); }
^
Csparse_reader.h:106:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curi<0 || curi>=NR) {
^
In file included from all_readers.h:8:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
simple_reader.h: In instantiation of ‘beachmat::simple_reader<T, V>::simple_reader(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99: required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::simple_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:181:100: required from ‘beachmat::simple_lin_matrix<T, V>::simple_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
numeric_matrix.cpp:63:78: required from here
simple_reader.h:59:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
In file included from all_readers.h:12:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
delayed_reader.h: In instantiation of ‘static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long unsigned int>&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
delayed_reader.h:115:19: required from ‘beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]’
delayed_reader.h:371:20: required from ‘beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; base_mat = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:92:99: required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::delayed_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage>, beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
numeric_matrix.cpp:57:87: required from here
delayed_reader.h:154:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 1 || i > original_dim) {
^
In file included from LIN_matrix.h:238:0,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
numeric_matrix.cpp:86:1: required from here
LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
In file included from all_readers.h:10:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
LIN_methods_read.h:120:5: required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’
numeric_matrix.cpp:86:1: required from here
Csparse_reader.h:208:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (idex!=*pIt && i[idex]==r) { (*out)=x[idex]; }
^
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = double*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
LIN_methods_read.h:126:5: required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]’
numeric_matrix.cpp:86:1: required from here
Csparse_reader.h:208:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_reader.h: In instantiation of ‘T beachmat::Csparse_reader<T, V>::get(size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
LIN_methods_read.h:132:27: required from ‘T beachmat::general_lin_matrix<T, V, RDR>::get(size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long unsigned int]’
numeric_matrix.cpp:86:1: required from here
Csparse_reader.h:121:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (loc!=iend && *loc==r) {
^
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<T, V>::update_indices(size_t, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
Csparse_reader.h:202:19: required from ‘void beachmat::Csparse_reader<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long unsigned int]’
LIN_methods_read.h:120:5: required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’
numeric_matrix.cpp:86:1: required from here
Csparse_reader.h:164:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex] < r) {
^
Csparse_reader.h:171:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex-1] >= r) {
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c output_param.cpp -o output_param.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c repacker.cpp -o repacker.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o beachmat.so HDF5_utils.o character_matrix.o character_output.o dim_checker.o find_chunks.o functions.o integer_matrix.o logical_matrix.o numeric_matrix.o output_param.o repacker.o utils.o /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
ar rc libbeachmat.a dim_checker.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o
g++ -std=gnu++11 -shared -L/usr/local/lib -o libbeachmat.so dim_checker.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o `echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "/home/biocbuild/bbs-3.8-bioc/R/bin/R" --vanilla --slave`
mkdir -p "/home/biocbuild/bbs-3.8-bioc-longtests/meat/beachmat.Rcheck/beachmat/lib" "/home/biocbuild/bbs-3.8-bioc-longtests/meat/beachmat.Rcheck/beachmat/include/beachmat"
cp dim_checker.h utils.h beachmat.h HDF5_utils.h output_param.h HDF5_reader.h Csparse_reader.h dense_reader.h simple_reader.h all_readers.h delayed_reader.h unknown_reader.h external_reader.h simple_writer.h Csparse_writer.h HDF5_writer.h all_writers.h LIN_matrix.h LIN_methods_read.h LIN_methods_write.h LIN_output.h logical_matrix.h integer_matrix.h character_matrix.h numeric_matrix.h character_output.h "/home/biocbuild/bbs-3.8-bioc-longtests/meat/beachmat.Rcheck/beachmat/include/beachmat"
mv libbeachmat.* "/home/biocbuild/bbs-3.8-bioc-longtests/meat/beachmat.Rcheck/beachmat/lib"
installing to /home/biocbuild/bbs-3.8-bioc-longtests/meat/beachmat.Rcheck/beachmat/libs
** R
** 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
* DONE (beachmat)