Jianqiang Sun
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/CircSeqAlignTk |
| git_branch: RELEASE_3_20 |
| git_last_commit: 710288a |
| git_last_commit_date: 2024-10-29 11:14:51 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
| 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 | ||||
| Package 356/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CircSeqAlignTk 1.8.0 (landing page) Jianqiang Sun
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: CircSeqAlignTk |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CircSeqAlignTk.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CircSeqAlignTk_1.8.0.tar.gz |
| StartedAt: 2024-12-19 21:30:56 -0500 (Thu, 19 Dec 2024) |
| EndedAt: 2024-12-19 21:41:43 -0500 (Thu, 19 Dec 2024) |
| EllapsedTime: 647.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CircSeqAlignTk.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CircSeqAlignTk.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CircSeqAlignTk_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CircSeqAlignTk.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 loading without being on the library search path ... 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
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.20-bioc/meat/CircSeqAlignTk.Rcheck/00check.log’
for details.
CircSeqAlignTk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CircSeqAlignTk ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)
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: x86_64-pc-linux-gnu
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: 00:00:01
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:
6968 (69.68%) aligned 0 times
3032 (30.32%) aligned exactly 1 time
0 (0.00%) aligned >1 times
30.32% overall alignment rate
6968 reads; of these:
6968 (100.00%) were unpaired; of these:
0 (0.00%) aligned 0 times
6968 (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
38.346 3.134 41.634
CircSeqAlignTk.Rcheck/CircSeqAlignTk-Ex.timings
| name | user | system | elapsed | |
| CircSeqAlignTk-package | 0.002 | 0.000 | 0.002 | |
| align_reads | 2.940 | 0.379 | 3.334 | |
| build_app | 0 | 0 | 0 | |
| build_index | 0.281 | 0.222 | 0.501 | |
| calc_coverage | 3.616 | 0.387 | 4.009 | |
| filter_reads | 1.686 | 0.006 | 1.693 | |
| generate_reads | 2.124 | 0.155 | 2.279 | |
| get_slot_contents | 0.500 | 0.001 | 0.501 | |
| merge.CircSeqAlignTkSim | 1.074 | 0.001 | 1.074 | |
| plot_coverage | 3.327 | 0.351 | 3.690 | |