Hervé Pagès
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/DelayedArray |
| git_branch: RELEASE_3_18 |
| git_last_commit: 4f63877 |
| git_last_commit_date: 2023-10-24 10:54:24 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:36 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 527/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DelayedArray 0.28.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the DelayedArray package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DelayedArray.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: DelayedArray |
| Version: 0.28.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:DelayedArray.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings DelayedArray_0.28.0.tar.gz |
| StartedAt: 2023-11-02 09:53:01 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 10:11:40 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 1119.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DelayedArray.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:DelayedArray.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings DelayedArray_0.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DelayedArray.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DelayedArray/DESCRIPTION’ ... OK
* this is package ‘DelayedArray’ version ‘0.28.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'stats4', 'Matrix', 'BiocGenerics', 'MatrixGenerics', 'S4Vectors',
'IRanges', 'S4Arrays', 'SparseArray'
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
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'inst/doc' contains invalid file names:
‘02-Implementing_a_backend.Rmd’ ‘01-Working_with_large_arrays.Rnw’
‘03-DelayedArray_HDF5Array_update.Rnw’
‘02-Implementing_a_backend.html’ ‘01-Working_with_large_arrays.pdf’
‘03-DelayedArray_HDF5Array_update.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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ... WARNING
Undocumented code objects:
‘defaultMultAutoGrids’ ‘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 '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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘DelayedArray-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RleArray-class
> ### Title: RleArray objects
> ### Aliases: class:RleArray RleArray-class RleArray
> ### DelayedArray,RleArraySeed-method coerce,RleArray,Rle-method
> ### class:RleMatrix RleMatrix-class RleMatrix matrixClass,RleArray-method
> ### coerce,RleArray,RleMatrix-method coerce,RleMatrix,RleArray-method
> ### coerce,ANY,RleMatrix-method coerce,RleList,RleArray-method
> ### coerce,RleMatrix,RleList-method coerce,DataFrame,RleArray-method
> ### coerce,RleMatrix,DataFrame-method
> ### coerce,DelayedMatrix,DataFrame-method
> ### write_block,RleRealizationSink-method
> ### coerce,RleRealizationSink,RleArray-method
> ### coerce,RleRealizationSink,DelayedArray-method
> ### coerce,ANY,RleArray-method coerce,DelayedArray,RleArray-method
> ### coerce,DelayedMatrix,RleMatrix-method
> ### Keywords: classes methods
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## A. BASIC EXAMPLE
> ## ---------------------------------------------------------------------
>
> data <- Rle(sample(6L, 500000, replace=TRUE), 8)
> a <- array(data, dim=c(50, 20, 4000)) # array() expands the Rle object
> # internally with as.vector()
>
> A <- RleArray(data, dim=c(50, 20, 4000)) # Rle object is NOT expanded
> A
<50 x 20 x 4000> RleArray object of type "integer":
,,1
[,1] [,2] [,3] [,4] ... [,17] [,18] [,19] [,20]
[1,] 1 6 5 5 . 3 4 2 6
[2,] 1 6 5 5 . 3 4 2 6
... . . . . . . . . .
[49,] 6 5 5 5 . 4 2 6 5
[50,] 6 5 5 5 . 4 2 6 5
...
,,4000
[,1] [,2] [,3] [,4] ... [,17] [,18] [,19] [,20]
[1,] 3 5 3 5 . 6 3 5 3
[2,] 3 5 3 5 . 6 3 5 3
... . . . . . . . . .
[49,] 5 3 5 1 . 3 5 3 6
[50,] 5 3 5 1 . 3 5 3 6
>
> object.size(a)
16000224 bytes
> object.size(A)
3335080 bytes
>
> stopifnot(identical(a, as.array(A)))
>
> as(A, "Rle") # deconstruction
integer-Rle of length 4000000 with 416534 runs
Lengths: 8 8 8 8 8 8 8 8 16 8 16 ... 16 16 8 8 8 8 8 8 8 8
Values : 1 4 1 2 5 3 6 2 3 1 5 ... 1 3 6 3 4 6 3 4 1 6
>
> toto <- function(x) (5 * x[ , , 1] ^ 3 + 1L) * log(x[, , 2])
> m1 <- toto(a)
> head(m1)
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] 10.75056 1187.6 433.91014 0.0000 56.83807 222.5002 352.6545 0.000000
[2,] 10.75056 1187.6 433.91014 0.0000 56.83807 222.5002 352.6545 0.000000
[3,] 10.75056 1187.6 433.91014 687.7313 56.83807 222.5002 352.6545 4.158883
[4,] 10.75056 1187.6 433.91014 687.7313 56.83807 222.5002 352.6545 4.158883
[5,] 10.75056 1187.6 73.46214 687.7313 56.83807 222.5002 352.6545 4.158883
[6,] 10.75056 1187.6 73.46214 687.7313 56.83807 222.5002 352.6545 4.158883
[,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 0 1936.892 1187.6 0.000000 516.6296 1121.641 1936.89199 575.1548
[2,] 0 1936.892 1187.6 0.000000 516.6296 1121.641 1936.89199 575.1548
[3,] 0 1936.892 1187.6 6.591674 516.6296 1121.641 1936.89199 243.6793
[4,] 0 1936.892 1187.6 6.591674 516.6296 1121.641 1936.89199 243.6793
[5,] 0 1936.892 0.0 6.591674 516.6296 1121.641 28.41903 243.6793
[6,] 0 1936.892 0.0 6.591674 516.6296 1121.641 28.41903 243.6793
[,17] [,18] [,19] [,20]
[1,] 188.536 352.6545 56.83807 0
[2,] 188.536 352.6545 56.83807 0
[3,] 188.536 352.6545 56.83807 0
[4,] 188.536 352.6545 56.83807 0
[5,] 188.536 352.6545 149.41127 0
[6,] 188.536 352.6545 149.41127 0
>
> M1 <- toto(A) # very fast! (operations are delayed)
> M1
<50 x 20> DelayedMatrix object of type "double":
[,1] [,2] [,3] ... [,19] [,20]
[1,] 10.75056 1187.59988 433.91014 . 56.83807 0.00000
[2,] 10.75056 1187.59988 433.91014 . 56.83807 0.00000
[3,] 10.75056 1187.59988 433.91014 . 56.83807 0.00000
[4,] 10.75056 1187.59988 433.91014 . 56.83807 0.00000
[5,] 10.75056 1187.59988 73.46214 . 149.41127 0.00000
... . . . . . .
[46,] 243.6793 867.8203 0.0000 . 0.0000 867.8203
[47,] 243.6793 433.9101 0.0000 . 0.0000 867.8203
[48,] 243.6793 433.9101 0.0000 . 0.0000 867.8203
[49,] 1187.5999 433.9101 0.0000 . 0.0000 867.8203
[50,] 1187.5999 433.9101 0.0000 . 0.0000 867.8203
>
> stopifnot(identical(m1, as.array(M1)))
>
> cs <- colSums(m1)
> CS <- colSums(M1)
> stopifnot(identical(cs, CS))
>
> ## Coercing a DelayedMatrix object to DataFrame produces a DataFrame
> ## object with Rle columns:
> as(M1, "DataFrame")
DataFrame with 50 rows and 20 columns
V1 V2 V3 V4
<Rle> <Rle> <Rle> <Rle>
1 10.7505568153683 1187.59988405023 433.910135030526 0
2 10.7505568153683 1187.59988405023 433.910135030526 0
3 10.7505568153683 1187.59988405023 433.910135030526 687.731292706237
4 10.7505568153683 1187.59988405023 433.910135030526 687.731292706237
5 10.7505568153683 1187.59988405023 73.4621382383502 687.731292706237
... ... ... ... ...
46 243.679287815015 867.820270061051 0 0
47 243.679287815015 433.910135030526 0 0
48 243.679287815015 433.910135030526 0 0
49 1187.59988405023 433.910135030526 0 0
50 1187.59988405023 433.910135030526 0 0
V5 V6 V7 V8
<Rle> <Rle> <Rle> <Rle>
1 56.8380688059155 222.500244959742 352.654544662463 0
2 56.8380688059155 222.500244959742 352.654544662463 0
3 56.8380688059155 222.500244959742 352.654544662463 4.15888308335967
4 56.8380688059155 222.500244959742 352.654544662463 4.15888308335967
5 56.8380688059155 222.500244959742 352.654544662463 4.15888308335967
... ... ... ... ...
46 4.15888308335967 1187.59988405023 0 218.883556091038
47 4.15888308335967 352.654544662463 0 218.883556091038
48 4.15888308335967 352.654544662463 0 218.883556091038
49 222.500244959742 352.654544662463 0 218.883556091038
50 222.500244959742 352.654544662463 0 218.883556091038
V9 V10 V11 V12
<Rle> <Rle> <Rle> <Rle>
1 0 1936.89198623553 1187.59988405023 0
2 0 1936.89198623553 1187.59988405023 0
3 0 1936.89198623553 1187.59988405023 6.59167373200866
4 0 1936.89198623553 1187.59988405023 6.59167373200866
5 0 1936.89198623553 0 6.59167373200866
... ... ... ... ...
46 73.4621382383502 0 0 0
47 73.4621382383502 1187.59988405023 0 0
48 73.4621382383502 1187.59988405023 0 0
49 1936.89198623553 1187.59988405023 0 0
50 1936.89198623553 1187.59988405023 0 0
V13 V14 V15 V16
<Rle> <Rle> <Rle> <Rle>
1 516.629569891346 1121.64142773676 1936.89198623553 575.154789622206
2 516.629569891346 1121.64142773676 1936.89198623553 575.154789622206
3 516.629569891346 1121.64142773676 1936.89198623553 243.679287815015
4 516.629569891346 1121.64142773676 1936.89198623553 243.679287815015
5 516.629569891346 1121.64142773676 28.4190344029578 243.679287815015
... ... ... ... ...
46 4.15888308335967 243.679287815015 575.154789622206 188.536033112305
47 4.15888308335967 1936.89198623553 575.154789622206 188.536033112305
48 4.15888308335967 1936.89198623553 575.154789622206 188.536033112305
49 1121.64142773676 1936.89198623553 575.154789622206 188.536033112305
50 1121.64142773676 1936.89198623553 575.154789622206 188.536033112305
V17 V18 V19 V20
<Rle> <Rle> <Rle> <Rle>
1 188.536033112305 352.654544662463 56.8380688059155 0
2 188.536033112305 352.654544662463 56.8380688059155 0
3 188.536033112305 352.654544662463 56.8380688059155 0
4 188.536033112305 352.654544662463 56.8380688059155 0
5 188.536033112305 352.654544662463 149.411271258863 0
... ... ... ... ...
46 0 243.679287815015 0 867.820270061051
47 0 56.8380688059155 0 867.820270061051
48 0 56.8380688059155 0 867.820270061051
49 352.654544662463 56.8380688059155 0 867.820270061051
50 352.654544662463 56.8380688059155 0 867.820270061051
>
> ## ---------------------------------------------------------------------
> ## B. MAKING AN RleArray OBJECT FROM A LIST-LIKE OBJECT OF Rle OBJECTS
> ## ---------------------------------------------------------------------
>
> ## From a DataFrame object:
> DF <- DataFrame(A=Rle(sample(3L, 100, replace=TRUE)),
+ B=Rle(sample(3L, 100, replace=TRUE)),
+ C=Rle(sample(3L, 100, replace=TRUE) - 0.5),
+ row.names=sprintf("ID%03d", 1:100))
>
> M2 <- RleArray(DF)
> M2
<100 x 3> RleMatrix object of type "double":
A B C
ID001 1.0 3.0 1.5
ID002 2.0 3.0 0.5
ID003 3.0 3.0 0.5
ID004 3.0 3.0 2.5
ID005 3.0 1.0 1.5
... . . .
ID096 2.0 3.0 2.5
ID097 3.0 1.0 1.5
ID098 1.0 1.0 2.5
ID099 2.0 1.0 0.5
ID100 2.0 3.0 2.5
>
> A3 <- RleArray(DF, dim=c(25, 6, 2))
> A3
<25 x 6 x 2> RleArray object of type "double":
,,1
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1 3 2 2 3 3
[2,] 2 1 2 2 3 1
... . . . . . .
[24,] 1 3 2 2 3 1
[25,] 3 3 2 2 3 2
,,2
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 2.0 3.0 1.5 2.5 0.5 0.5
[2,] 3.0 3.0 0.5 1.5 0.5 2.5
... . . . . . .
[24,] 2.0 1.0 2.5 1.5 1.5 0.5
[25,] 3.0 3.0 2.5 0.5 1.5 2.5
>
> M4 <- RleArray(DF, dim=c(25, 12), dimnames=list(LETTERS[1:25], NULL))
> M4
<25 x 12> RleMatrix object of type "double":
[,1] [,2] [,3] ... [,11] [,12]
A 1 3 2 . 0.5 0.5
B 2 1 2 . 0.5 2.5
C 3 1 1 . 0.5 0.5
D 3 3 2 . 2.5 1.5
E 3 1 2 . 2.5 0.5
. . . . . . .
U 2 2 3 . 0.5 2.5
V 2 3 2 . 2.5 1.5
W 3 3 2 . 0.5 2.5
X 1 3 2 . 1.5 0.5
Y 3 3 2 . 1.5 2.5
>
> ## From an ordinary list:
> ## If all the supplied Rle objects have the same length and if the 'dim'
> ## argument is not specified, then the RleArray() constructor returns an
> ## RleMatrix object with 1 column per Rle object. If the 'dimnames'
> ## argument is not specified, then the names on the list are propagated
> ## as the colnames of the returned object.
> data <- as.list(DF)
> M2b <- RleArray(data)
> A3b <- RleArray(data, dim=c(25, 6, 2))
> M4b <- RleArray(data, dim=c(25, 12), dimnames=list(LETTERS[1:25], NULL))
>
> data2 <- list(Rle(sample(3L, 9, replace=TRUE)) * 11L,
+ Rle(sample(3L, 15, replace=TRUE)))
> ## Not run:
> ##D RleArray(data2) # error! (cannot infer the dim)
> ## End(Not run)
> RleArray(data2, dim=c(4, 6))
<4 x 6> RleMatrix object of type "integer":
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 22 22 22 1 3 3
[2,] 22 22 3 3 2 2
[3,] 33 22 1 1 3 3
[4,] 11 33 3 2 2 1
>
> ## From an RleList object:
> data <- RleList(data)
> M2c <- RleArray(data)
> A3c <- RleArray(data, dim=c(25, 6, 2))
> M4c <- RleArray(data, dim=c(25, 12), dimnames=list(LETTERS[1:25], NULL))
>
> data2 <- RleList(data2)
> ## Not run:
> ##D RleArray(data2) # error! (cannot infer the dim)
> ## End(Not run)
> RleArray(data2, dim=4:2)
<4 x 3 x 2> RleArray object of type "integer":
,,1
[,1] [,2] [,3]
[1,] 22 22 22
[2,] 22 22 3
[3,] 33 22 1
[4,] 11 33 3
,,2
[,1] [,2] [,3]
[1,] 1 3 3
[2,] 3 2 2
[3,] 1 3 3
[4,] 2 2 1
>
> ## Sanity checks:
> data0 <- as.vector(unlist(DF, use.names=FALSE))
> m2 <- matrix(data0, ncol=3, dimnames=dimnames(M2))
> stopifnot(identical(m2, as.matrix(M2)))
> rownames(m2) <- NULL
> stopifnot(identical(m2, as.matrix(M2b)))
> stopifnot(identical(m2, as.matrix(M2c)))
> a3 <- array(data0, dim=c(25, 6, 2))
> stopifnot(identical(a3, as.array(A3)))
> stopifnot(identical(a3, as.array(A3b)))
> stopifnot(identical(a3, as.array(A3c)))
> m4 <- matrix(data0, ncol=12, dimnames=dimnames(M4))
> stopifnot(identical(m4, as.matrix(M4)))
> stopifnot(identical(m4, as.matrix(M4b)))
> stopifnot(identical(m4, as.matrix(M4c)))
>
> ## ---------------------------------------------------------------------
> ## C. COERCING FROM RleList OR DataFrame TO RleMatrix
> ## ---------------------------------------------------------------------
>
> ## Coercing an RleList object to RleMatrix only works if all the list
> ## elements in the former have the same length.
> x <- RleList(A=Rle(sample(3L, 20, replace=TRUE)),
+ B=Rle(sample(3L, 20, replace=TRUE)))
> M <- as(x, "RleMatrix")
> stopifnot(identical(x, as(M, "RleList")))
>
> x <- DataFrame(A=x[[1]], B=x[[2]], row.names=letters[1:20])
> M <- as(x, "RleMatrix")
> stopifnot(identical(x, as(M, "DataFrame")))
>
> ## ---------------------------------------------------------------------
> ## D. CONSTRUCTING A LARGE RleArray OBJECT
> ## ---------------------------------------------------------------------
>
> ## The RleArray() constructor does not accept a "long" Rle object (i.e.
> ## an object of length > .Machine$integer.max) at the moment:
> ## Not run:
> ##D RleArray(Rle(5, 3e9), dim=c(3, 1e9)) # error!
> ## End(Not run)
>
> ## The workaround is to supply a list of Rle objects instead:
>
> toy_Rle <- function() {
+ run_lens <- c(sample(4), sample(rep(c(1:19, 40) * 3, 6e4)), sample(4))
+ run_vals <- sample(700, length(run_lens), replace=TRUE) / 5
+ Rle(run_vals, run_lens)
+ }
> rle_list <- lapply(1:80, function(j) toy_Rle()) # takes about 20 sec.
* 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: 1 ERROR, 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/DelayedArray.Rcheck/00check.log’
for details.
DelayedArray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL DelayedArray ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘DelayedArray’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_DelayedArray.c -o R_init_DelayedArray.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c compress_atomic_vector.c -o compress_atomic_vector.o gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o compress_atomic_vector.o -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-DelayedArray/00new/DelayedArray/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘apply’ in package ‘DelayedArray’ Creating a new generic function for ‘sweep’ in package ‘DelayedArray’ Creating a new generic function for ‘scale’ 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’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DelayedArray)
DelayedArray.Rcheck/tests/run_unitTests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> require("DelayedArray") || stop("unable to load DelayedArray package")
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, append,
as.data.frame, basename, cbind, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind
Attaching package: 'S4Arrays'
The following object is masked from 'package:abind':
abind
The following object is masked from 'package:base':
rowsum
Loading required package: SparseArray
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, scale, sweep
[1] TRUE
> DelayedArray:::.test()
Attaching package: 'genefilter'
The following object is masked from 'package:DelayedArray':
rowVars
The following objects are masked from 'package:SparseArray':
rowSds, rowVars
The following objects are masked from 'package:MatrixGenerics':
rowSds, rowVars
The following objects are masked from 'package:matrixStats':
rowSds, rowVars
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, append,
as.data.frame, basename, cbind, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind
Attaching package: 'S4Arrays'
The following object is masked from 'package:abind':
abind
The following object is masked from 'package:base':
rowsum
Loading required package: SparseArray
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, scale, sweep
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, append,
as.data.frame, basename, cbind, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind
Attaching package: 'S4Arrays'
The following object is masked from 'package:abind':
abind
The following object is masked from 'package:base':
rowsum
Loading required package: SparseArray
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, scale, sweep
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, append,
as.data.frame, basename, cbind, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind
Attaching package: 'S4Arrays'
The following object is masked from 'package:abind':
abind
The following object is masked from 'package:base':
rowsum
Loading required package: SparseArray
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, scale, sweep
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, append,
as.data.frame, basename, cbind, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind
Attaching package: 'S4Arrays'
The following object is masked from 'package:abind':
abind
The following object is masked from 'package:base':
rowsum
Loading required package: SparseArray
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, scale, sweep
Error in S4Arrays:::normarg_perm(perm, dim(seed)) :
'perm' must be an integer vector
In addition: Warning messages:
1: In log(a + 0.2) : NaNs produced
2: In OP(a) : NaNs produced
Error in validObject(.Object) : invalid class "DelayedAperm" object:
'perm' cannot be an empty vector
Error in validObject(.Object) : invalid class "DelayedAperm" object:
only dimensions with an extent of 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 with an extent of 1 can be dropped
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 S4Arrays:::normarg_dimnames(dimnames, seed_dim) :
the supplied 'dimnames' must be NULL or a list
Error in S4Arrays:::normarg_dimnames(dimnames, seed_dim) :
the supplied 'dimnames' must have one list element per dimension
Error in FUN(X[[i]], ...) :
each list element in the supplied 'dimnames' must be NULL or a
character vector
Error in FUN(X[[i]], ...) :
length of 'dimnames[[1]]' (26) must equal the array extent (5)
Error in S4Arrays:::normalize_Nindex(Nindex, seed) :
'Nindex' must be a list with one list element per dimension in 'x'
Error in S4Arrays:::normalize_Nindex(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
RUNIT TEST PROTOCOL -- Thu Nov 2 10:11:35 2023
***********************************************
Number of test functions: 47
Number of errors: 0
Number of failures: 0
1 Test Suite :
DelayedArray RUnit Tests - 47 test functions, 0 errors, 0 failures
Number of test functions: 47
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
785.500 20.789 876.368
DelayedArray.Rcheck/DelayedArray-Ex.timings
| name | user | system | elapsed | |
| AutoBlock-global-settings | 0.264 | 0.000 | 0.264 | |
| AutoGrid | 2.128 | 0.100 | 2.234 | |
| ConstantArray-class | 0.062 | 0.020 | 0.082 | |
| DelayedAbind-class | 0.138 | 0.016 | 0.154 | |
| DelayedAperm-class | 0.047 | 0.004 | 0.051 | |
| DelayedArray-class | 8.485 | 0.243 | 8.773 | |
| DelayedArray-stats | 2.163 | 0.026 | 2.195 | |
| DelayedArray-utils | 13.179 | 0.772 | 15.466 | |
| DelayedMatrix-stats | 2.698 | 0.168 | 2.883 | |
| DelayedMatrix-utils | 21.102 | 1.915 | 24.171 | |
| DelayedNaryIsoOp-class | 0.057 | 0.000 | 0.059 | |
| DelayedSetDimnames-class | 0.028 | 0.000 | 0.028 | |
| DelayedSubassign-class | 0.082 | 0.000 | 0.082 | |
| DelayedSubset-class | 0.078 | 0.000 | 0.079 | |
| DelayedUnaryIsoOpStack-class | 0.077 | 0.007 | 0.085 | |
| DelayedUnaryIsoOpWithArgs-class | 0.199 | 0.000 | 0.198 | |
| RealizationSink-class | 3.374 | 0.095 | 3.479 | |