- using R Under development (unstable) (2025-02-28 r87840)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (Debian 14.2.0-16) 14.2.0
GNU Fortran (Debian 14.2.0-16) 14.2.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘restez/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘restez’ version ‘2.1.4’
- 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 executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking serialization versions ... OK
- checking whether package ‘restez’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] OK
- checking use of S3 registration ... 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 ... [4s/6s] OK
- checking Rd files ... [1s/1s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... 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 contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking examples ... [7s/12s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [21s/32s] ERROR
Running ‘test-all.R’ [21s/32s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("restez")
Loading required package: restez
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Inspecting 1 file(s) to add to the database ...
... 'test.seq.gz' (1/1)
Done.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Inspecting 1 file(s) to add to the database ...
... 'test.seq.gz' (1/1)
Done.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
────────────────────────────────────────────────────────────────────────────────
Looking up latest GenBank release ...
... release number 1000
... found 1 sequence files
────────────────────────────────────────────────────────────────────────────────
Which sequence file types would you like to download?
Choose from those listed below:
• 1 - 'type1'
1 files and 1e-07 GB
Provide one or more numbers separated by spaces.
e.g. to download all Mammalian sequences, type: "" followed by Enter
Which files would you like to download?
────────────────────────────────────────────────────────────────────────────────
You've selected a total of 1 file(s) and 1e-07 GB of uncompressed data.
These represent:
• 'type1'
Based on stated GenBank files sizes, we estimate ...
... 2e-08 GB for compressed, downloaded files
... 1.22e-07 GB for the SQL database
Leading to a total of 1.42e-07 GB
Please note, the real sizes of the database and its downloads cannot be
accurately predicted beforehand.
These are just estimates, actual sizes may differ by up to a factor of two.
Is this OK?
────────────────────────────────────────────────────────────────────────────────
Downloading ...
... 'file1.seq' (1/1)
Done. Enjoy your day.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... '1' (1/10)
... ... Hmmmm... no records found in that file.
... '2' (2/10)
... ... Hmmmm... no records found in that file.
... '3' (3/10)
... ... Hmmmm... no records found in that file.
... '4' (4/10)
... ... Hmmmm... no records found in that file.
... '5' (5/10)
... ... Hmmmm... no records found in that file.
... '6' (6/10)
... ... Hmmmm... no records found in that file.
... '7' (7/10)
... ... Hmmmm... no records found in that file.
... '8' (8/10)
... ... Hmmmm... no records found in that file.
... '9' (9/10)
... ... Hmmmm... no records found in that file.
... '10' (10/10)
... ... Hmmmm... no records found in that file.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... ... Your database is out-of-date. Latest release is 256
... ... Your database is up-to-date
example text example text'example text'example text
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Checking setup status at ...
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Checking setup status at ...
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'No'
... Total size NA
... Does the database have data? 'No'
... Number of sequences 0
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
Checking setup status at ...
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'Yes'
... Total size 780K
... Does the database have data? 'Yes'
... Number of sequences 10
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'No'
... Total size NA
... Does the database have data? 'No'
... Number of sequences 0
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
[ FAIL 1 | WARN 1 | SKIP 2 | PASS 138 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-db-tools.R:138:3'
• On Linux (1): 'test-db-tools.R:79:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get-tools.R:36:3'): gb_sequence_get() works ──────────────────
names(seq_dnabin_2) not equal to `id_2`.
2/2 mismatches
x[1]: "AC090938"
y[1]: "NR_040059"
x[2]: "NR_040059"
y[2]: "AC090938"
[ FAIL 1 | WARN 1 | SKIP 2 | PASS 138 ]
Error: Test failures
Execution halted
- checking PDF version of manual ... [10s/12s] OK
- checking HTML version of manual ... [4s/7s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR