Multiple platform build/check report for BioC 3.20 - CHECK results for CircSeqAlignTk on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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*

CHECK results for CircSeqAlignTk on kjohnson1

To the developers/maintainers of the CircSeqAlignTk package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CircSeqAlignTk.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.

raw results

Summary

Package: CircSeqAlignTk

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CircSeqAlignTk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CircSeqAlignTk_1.8.0.tar.gz

StartedAt: 2024-12-20 14:37:04 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 14:44:20 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 436.1 seconds

RetCode: 0

Status: OK

CheckDir: CircSeqAlignTk.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CircSeqAlignTk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CircSeqAlignTk_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CircSeqAlignTk.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CircSeqAlignTk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CircSeqAlignTk’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CircSeqAlignTk’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
calc_coverage 5.846  0.575   6.585
plot_coverage 5.196  0.528   5.854
align_reads   4.829  0.562   5.705
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CircSeqAlignTk.Rcheck/00check.log’
for details.

Installation output

CircSeqAlignTk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CircSeqAlignTk
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘CircSeqAlignTk’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CircSeqAlignTk)

Tests output

CircSeqAlignTk.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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('CircSeqAlignTk')
> test_check('CircSeqAlignTk')
Building a SMALL index
Building a SMALL index
29178 reads; of these:
  29178 (100.00%) were unpaired; of these:
    29012 (99.43%) aligned 0 times
    166 (0.57%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.57% overall alignment rate
29012 reads; of these:
  29012 (100.00%) were unpaired; of these:
    28981 (99.89%) aligned 0 times
    31 (0.11%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.11% overall alignment rate
29178 reads; of these:
  29178 (100.00%) were unpaired; of these:
    29012 (99.43%) aligned 0 times
    166 (0.57%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.57% overall alignment rate
29012 reads; of these:
  29012 (100.00%) were unpaired; of these:
    28981 (99.89%) aligned 0 times
    31 (0.11%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.11% overall alignment rate
Settings:
  Output files: "tmp_ht2index/refseq.t1.*.ht2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Local offset rate: 3 (one in 8)
  Local fTable chars: 6
  Local sequence length: 57344
  Local sequence overlap between two consecutive indexes: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  tmp_ht2index/refseq.t1.fa
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 68 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 68 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 70
fchr[G]: 180
fchr[T]: 281
fchr[$]: 361
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 4194625 bytes to primary GFM file: tmp_ht2index/refseq.t1.1.ht2
Wrote 96 bytes to secondary GFM file: tmp_ht2index/refseq.t1.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 8421 bytes to primary GFM file: tmp_ht2index/refseq.t1.5.ht2
Wrote 96 bytes to secondary GFM file: tmp_ht2index/refseq.t1.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
    len: 361
    gbwtLen: 362
    nodes: 362
    sz: 91
    gbwtSz: 91
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 23
    offsSz: 92
    lineSz: 64
    sideSz: 64
    sideGbwtSz: 48
    sideGbwtLen: 192
    numSides: 2
    numLines: 2
    gbwtTotLen: 128
    gbwtTotSz: 128
    reverse: 0
    linearFM: Yes
Total time for call to driver() for forward index: 00:00:00
Settings:
  Output files: "tmp_ht2index/refseq.t2.*.ht2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Local offset rate: 3 (one in 8)
  Local fTable chars: 6
  Local sequence length: 57344
  Local sequence overlap between two consecutive indexes: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  tmp_ht2index/refseq.t2.fa
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 68 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 68 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 70
fchr[G]: 180
fchr[T]: 281
fchr[$]: 361
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 4194625 bytes to primary GFM file: tmp_ht2index/refseq.t2.1.ht2
Wrote 96 bytes to secondary GFM file: tmp_ht2index/refseq.t2.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 8421 bytes to primary GFM file: tmp_ht2index/refseq.t2.5.ht2
Wrote 96 bytes to secondary GFM file: tmp_ht2index/refseq.t2.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
    len: 361
    gbwtLen: 362
    nodes: 362
    sz: 91
    gbwtSz: 91
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 23
    offsSz: 92
    lineSz: 64
    sideSz: 64
    sideGbwtSz: 48
    sideGbwtLen: 192
    numSides: 2
    numLines: 2
    gbwtTotLen: 128
    gbwtTotSz: 128
    reverse: 0
    linearFM: Yes
Total time for call to driver() for forward index: 00:00:00
29178 reads; of these:
  29178 (100.00%) were unpaired; of these:
    29007 (99.41%) aligned 0 times
    171 (0.59%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.59% overall alignment rate
29007 reads; of these:
  29007 (100.00%) were unpaired; of these:
    28978 (99.90%) aligned 0 times
    29 (0.10%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.10% overall alignment rate
29178 reads; of these:
  29178 (100.00%) were unpaired; of these:
    29007 (99.41%) aligned 0 times
    171 (0.59%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.59% overall alignment rate
29007 reads; of these:
  29007 (100.00%) were unpaired; of these:
    28978 (99.90%) aligned 0 times
    29 (0.10%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.10% overall alignment rate
Building a SMALL index
Building a SMALL index
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    10000 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
0 reads
0.00% overall alignment rate
Building a SMALL index
Building a SMALL index
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    6893 (68.93%) aligned 0 times
    3107 (31.07%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
31.07% overall alignment rate
6893 reads; of these:
  6893 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    6893 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
Building a SMALL index
Building a SMALL index
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    839 (8.39%) aligned 0 times
    9161 (91.61%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
91.61% overall alignment rate
839 reads; of these:
  839 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    839 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    1846 (18.46%) aligned 0 times
    8154 (81.54%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
81.54% overall alignment rate
1846 reads; of these:
  1846 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    1846 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    10000 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
0 reads
0.00% overall alignment rate
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    14 (0.14%) aligned 0 times
    9986 (99.86%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
99.86% overall alignment rate
14 reads; of these:
  14 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    14 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    10000 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
0 reads
0.00% overall alignment rate
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    1041 (10.41%) aligned 0 times
    8959 (89.59%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
89.59% overall alignment rate
1041 reads; of these:
  1041 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    1041 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    10000 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
0 reads
0.00% overall alignment rate
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    204 (2.04%) aligned 0 times
    9796 (97.96%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
97.96% overall alignment rate
204 reads; of these:
  204 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    204 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    3269 (32.69%) aligned 0 times
    6731 (67.31%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
67.31% overall alignment rate
3269 reads; of these:
  3269 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    3269 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    10000 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
0 reads
0.00% overall alignment rate
[ FAIL 0 | WARN 19 | SKIP 4 | PASS 2 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• empty test (4): 'test_workflow.R:1:1', 'test_workflow.R:16:1',
  'test_workflow.R:35:1', 'test_workflow.R:56:1'

[ FAIL 0 | WARN 19 | SKIP 4 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 55.542   5.977  64.464

Example timings

CircSeqAlignTk.Rcheck/CircSeqAlignTk-Ex.timings

name	user	system	elapsed
CircSeqAlignTk-package	0.003	0.001	0.005
align_reads	4.829	0.562	5.705
build_app	0.000	0.000	0.001
build_index	0.352	0.169	0.545
calc_coverage	5.846	0.575	6.585
filter_reads	2.723	0.031	2.765
generate_reads	2.685	0.172	2.866
get_slot_contents	0.625	0.009	0.637
merge.CircSeqAlignTkSim	1.617	0.041	1.665
plot_coverage	5.196	0.528	5.854