* using log directory ‘/srv/hornik/tmp/CRAN/geno2proteo.Rcheck’
* using R Under development (unstable) (2023-11-02 r85465)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (16)
    GNU Fortran (Debian 13.2.0-5) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘geno2proteo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geno2proteo’ version ‘0.0.7’
* checking CRAN incoming feasibility ... [3s/4s] Note_to_CRAN_maintainers
Maintainer: ‘Yaoyong Li<liyaoyong85@gmail.com>’
* 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 ‘geno2proteo’ can be installed ... [7s/7s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... NOTE
Problems with news in ‘NEWS’:
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    give the temporary file a name based on the current time
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    and a random number, instead of a fixed file name, in order to deal with 
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    the situation in which more than processes are run at the same time.
    2. Added the codes to the functions genomicLocsToWholeDNASequence(), 
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    genomicLocsToProteinSequence() and proteinLocsToGenomic() to make sure
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    the start position is not greater than the end position in the regions. 
    3. Made one change in the document Vignettes (in Section 3) to state that 
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    with the case that the input file contains some protein ID(s) which are not
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    in the gene annotation file and hence are not in the CDSaaFile used by the 
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    function. Accordingly, added one row at the end of the test data file
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    of the function
     transId_pfamDomainStartEnd_chr16_Zdomains_22examples_proteinID.txt 
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    for one protein ID which is not in any CDSaaFile in order to test the 
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    added code.
    2. Made one change in the document Vignettes (in Section 1) to state that the 
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    package is in the CRAN repository.  
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    with the case that there is no overlap between the input genomic loci and the
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    protein coding genes, by returning a data frame with the genomic regions and 
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    result columns filled with NAs, instead of a short message.
    2. Still in the function genomicLocsToProteinSequence(), it now outputs all the amino
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    acids coded by the DNA bases. In the previous version it did not output the amino acid coded 
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    by the last DNA bases if it needs some more DNA base after the current DNA sequences, which
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    looks not that intuitive.
    3. Updated the introduction document (vignette) of the package.
    4. Fixed an error caused by a new toolchain on Windows in which Perl installed on the system 
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    does not automatically convert newlines on input to LF. The fix method had been
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    proposed by the maintainers of CRAN repository who encountered the issue at the first place,
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    which was to replace all the "chomp;" in the two Perl scripts by "s/[\r\n]+//;".
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    with the case that there is no overlap between the input genomic loci and the
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    protein coding genes.  
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    files in the folders that they should not be created, more modifications were done
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    in this version, namely putting the DNA sequence file uncompressed from the 
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    gz file to the temporary folder.
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    genomicLocsToWholeDNASequence, in order to keep them consistent with other
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    function names.
    2. Removed "utils" from the import list in DESCRIPTION file, because it is not
     used by the package.
    3. Addressed the issue of creating and writting some files in the folders that
     they should not be created, as raised by the CRAN staff, by using the temporary
     folder obtained by tempdir(). 
  Cannot process chunk/lines:
    September - November 2017: the package was tested and reviewed.
  Cannot process chunk/lines:
    January - May 2017: the package was written.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [10s/10s] OK
* checking Rd files ... [0s/0s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [4s/4s] OK
  Running ‘runTests.R’ [4s/4s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [5s/5s] OK
* checking PDF version of manual ... [3s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE