Package: DelayedArray

Version: 0.9.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DelayedArray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DelayedArray_0.9.9.tar.gz

StartedAt: 2019-04-09 00:22:09 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:31:39 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 570.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DelayedArray.Rcheck

Warnings: 2

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DelayedArray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DelayedArray_0.9.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DelayedArray.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DelayedArray/DESCRIPTION’ ... OK
* this is package ‘DelayedArray’ version ‘0.9.9’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'stats4', 'matrixStats', 'BiocGenerics', 'S4Vectors', 'IRanges',
  'BiocParallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘DelayedArray’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Matrix’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'inst/doc' contains invalid file names:
  ‘02-Implementing_a_backend.Rmd’ ‘01-Working_with_large_arrays.Rnw’
  ‘02-Implementing_a_backend.html’ ‘01-Working_with_large_arrays.pdf’
Please remove or rename the files.
See section ‘Package subdirectories’ in the ‘Writing R Extensions’
manual.
* 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 objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘BiocGenerics:::testPackage’
  ‘S4Vectors:::.list.names’ ‘S4Vectors:::anyMissing’
  ‘S4Vectors:::anyMissingOrOutside’ ‘S4Vectors:::delete_NULLs’
  ‘S4Vectors:::diffWithInitialZero’
  ‘S4Vectors:::extract_positions_from_Rle’ ‘S4Vectors:::new_DataFrame’
  ‘S4Vectors:::prepare_objects_to_bind’
  ‘S4Vectors:::rep.int_along_ROWS’ ‘S4Vectors:::sapply_isNULL’
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
Undocumented code objects:
  ‘multGrids’
Undocumented S4 methods:
  generic '[' and siglist 'DelayedArray,ANY,ANY,ANY'
  generic '[<-' and siglist 'DelayedArray,ANY,ANY,ANY'
  generic 'crossprod' and siglist 'ANY,DelayedMatrix'
  generic 'crossprod' and siglist 'DelayedMatrix,ANY'
  generic 'crossprod' and siglist 'DelayedMatrix,DelayedMatrix'
  generic 'crossprod' and siglist 'DelayedMatrix,missing'
  generic 'dimnames<-' and siglist 'DelayedArray,ANY'
  generic 'tcrossprod' and siglist 'ANY,DelayedMatrix'
  generic 'tcrossprod' and siglist 'DelayedMatrix,ANY'
  generic 'tcrossprod' and siglist 'DelayedMatrix,DelayedMatrix'
  generic 'tcrossprod' and siglist 'DelayedMatrix,missing'
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 for code/documentation mismatches ... OK
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
DelayedMatrix-utils 37.216  8.362  39.781
DelayedArray-utils  11.789  0.746  12.592
DelayedArray-class   7.139  0.549   7.718
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.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: 2 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/DelayedArray.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DelayedArray
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DelayedArray’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_DelayedArray.c -o R_init_DelayedArray.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c abind.c -o abind.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c compress_atomic_vector.c -o compress_atomic_vector.o
compress_atomic_vector.c:66:9: warning: variable 'ans' is uninitialized when used here [-Wuninitialized]
        return ans;
               ^˜˜
compress_atomic_vector.c:64:10: note: initialize the variable 'ans' to silence this warning
        SEXP ans;
                ^
                 = NULL
compress_atomic_vector.c:73:9: warning: variable 'ans' is uninitialized when used here [-Wuninitialized]
        return ans;
               ^˜˜
compress_atomic_vector.c:71:10: note: initialize the variable 'ans' to silence this warning
        SEXP ans;
                ^
                 = NULL
compress_atomic_vector.c:85:9: warning: variable 'ans' is uninitialized when used here [-Wuninitialized]
        return ans;
               ^˜˜
compress_atomic_vector.c:83:10: note: initialize the variable 'ans' to silence this warning
        SEXP ans;
                ^
                 = NULL
compress_atomic_vector.c:92:9: warning: variable 'ans' is uninitialized when used here [-Wuninitialized]
        return ans;
               ^˜˜
compress_atomic_vector.c:90:10: note: initialize the variable 'ans' to silence this warning
        SEXP ans;
                ^
                 = NULL
4 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o abind.o compress_atomic_vector.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/DelayedArray/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘aperm’ in package ‘DelayedArray’
Creating a generic function for ‘sweep’ from package ‘base’ in package ‘DelayedArray’
Creating a new generic function for ‘apply’ in package ‘DelayedArray’
Creating a new generic function for ‘rowsum’ in package ‘DelayedArray’
Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a new generic function for ‘rowMaxs’ in package ‘DelayedArray’
Creating a new generic function for ‘colMaxs’ in package ‘DelayedArray’
Creating a new generic function for ‘rowMins’ in package ‘DelayedArray’
Creating a new generic function for ‘colMins’ in package ‘DelayedArray’
Creating a new generic function for ‘rowRanges’ in package ‘DelayedArray’
Creating a new generic function for ‘colRanges’ in package ‘DelayedArray’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DelayedArray)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> require("DelayedArray") || stop("unable to load DelayedArray package")
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

[1] TRUE
> DelayedArray:::.test()
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
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automatic block size set to 40 bytes (was 24)
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automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
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automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
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automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
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automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
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automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
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automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
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automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
automatic block size set to 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
automatic block size set to 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
automatic block size set to 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
automatic block size set to 12 bytes (was 1e+08)
automatic block size set to 20 bytes (was 12)
automatic block size set to 50 bytes (was 20)
automatic block size set to 15000 bytes (was 50)
automatic block size set to 1e+08 bytes (was 15000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 24 bytes (was 30000)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)

Attaching package: 'genefilter'

The following objects are masked from 'package:matrixStats':

    rowSds, rowVars

automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
automatic block size set to 24 bytes (was 1e+08)
automatic block size set to 40 bytes (was 24)
automatic block size set to 100 bytes (was 40)
automatic block size set to 30000 bytes (was 100)
automatic block size set to 1e+08 bytes (was 30000)
Error in normarg_perm(perm, dim(seed)) : 'perm' must be an integer vector
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    'perm' cannot be an empty vector
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    only dimensions equal to 1 can be dropped
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    all non-NA values in 'perm' must be >= 1 and <= 'length(dim(a))'
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    only dimensions equal to 1 can be dropped
Error in .normalize_dimnames(dimnames, seed_ndim) : 
  the supplied dimnames must be a list
Error in .normalize_dimnames(dimnames, seed_ndim) : 
  the supplied dimnames must have one list element per dimension in the
  array-like object
Error in .normalize_dimnames(dimnames, seed_ndim) : 
  the supplied dimnames must have one list element per dimension in the
  array-like object
Error in validObject(.Object) : invalid class "DelayedDimnames" object: 
    each list element in 'x@dimnames' must be NULL, or a character vector
    of length the extent of the corresponding dimension, or special value
    -1
Error in validObject(.Object) : invalid class "DelayedDimnames" object: 
    each list element in 'x@dimnames' must be NULL, or a character vector
    of length the extent of the corresponding dimension, or special value
    -1
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at
  the moment. Note that you can check the number of seeds with nseed().
  You can use 'seedApply(x, identity)' to extract all the seeds as a
  list.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in match.fun(OP) : 'NULL' is not a function, character or symbol
Error in match.fun(OP) : 
  'list(NULL)' is not a function, character or symbol
Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'not-an-existing-function' of mode 'function' was not found
Error in new_DelayedNaryIsoOp("<=", array(dim = 4:2), array(dim = 2:4)) : 
  non-conformable array-like objects
Error in normalizeNindex(Nindex, seed) : 
  'Nindex' must be a list with one list element per dimension in 'x'
Error in normalizeNindex(Nindex, seed) : 
  'Nindex' must be a list with one list element per dimension in 'x'
Error : subscript contains out-of-bounds indices
Error : subscript contains invalid names
Error : subscript contains out-of-bounds ranges
Error : subscript contains out-of-bounds ranges
Error in new_DelayedUnaryIsoOpStack(.TEST_SAS3, NULL) : 
  'OPS' must be a list
Error in FUN(X[[i]], ...) : 
  'OPS[[1L]]' is not a function, character or symbol
Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'not-an-existing-function' of mode 'function' was not found
automatic block size set to 1e+07 bytes (was 1e+08)
automatic block size set to 1e+08 bytes (was 1e+07)


RUNIT TEST PROTOCOL -- Tue Apr  9 00:31:30 2019 
*********************************************** 
Number of test functions: 42 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DelayedArray RUnit Tests - 42 test functions, 0 errors, 0 failures
Number of test functions: 42 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
424.199 119.560 376.008 

name	user	system	elapsed
Array-class	0.002	0.001	0.004
ArrayGrid-class	0.474	0.019	0.495
DelayedArray-class	7.139	0.549	7.718
DelayedArray-stats	2.221	0.220	2.452
DelayedArray-utils	11.789	0.746	12.592
DelayedMatrix-stats	3.472	0.583	4.067
DelayedMatrix-utils	37.216	8.362	39.781
RealizationSink-class	1.052	0.156	1.214
RleArray-class	2.220	0.215	2.465
SparseArraySeed-class	0.389	0.133	0.524
bind-arrays	0.003	0.002	0.004
blockGrid	0.569	0.117	0.688
block_processing	0.034	0.028	0.108
chunkGrid	0.000	0.000	0.001
extract_array	0	0	0
linearInd	0.004	0.008	0.012
makeCappedVolumeBox	0.217	0.037	0.256
mapToGrid	0.028	0.005	0.034
read_block	0.198	0.025	0.225
realize	2.210	0.444	2.672
showtree	0.325	0.061	0.386
simplify	0.697	0.006	0.709