* using log directory ‘/srv/hornik/tmp/CRAN/PGRdup.Rcheck’ * using R Under development (unstable) (2019-09-18 r77193) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘PGRdup/DESCRIPTION’ ... OK * this is package ‘PGRdup’ version ‘0.2.3.4’ * package encoding: latin1 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘J. Aravind ’ * 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 ‘PGRdup’ can be installed ... [6s/6s] WARNING Found the following significant warnings: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] See ‘/srv/hornik/tmp/CRAN/PGRdup.Rcheck/00install.out’ for details. * 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 ... OK * 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 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 ... 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [2s/2s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [34s/28s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING Current CRAN status: ERROR: 4, WARN: 2, OK: 6 See: Version: 0.2.3.3 Check: examples, Result: ERROR Running examples in 'PGRdup-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: MergeKW > ### Title: Merge keyword strings > ### Aliases: MergeKW MergePrefix MergeSuffix > > ### ** Examples > > names <- c("Punjab Bold", "Gujarat- Dwarf", "Nagpur.local", "SAM COL 144", + "SAM COL--280", "NIZAMABAD-LOCAL", "Dark Green Mutant", + "Dixie-Giant", "Georgia- Bunch", "Uganda-erect", "Small Japan", + "Castle Cary", "Punjab erect", "Improved small japan", + "Dark Purple") > > # Merge pairs of strings > y1 <- list(c("Gujarat", "Dwarf"), c("Castle", "Cary"), c("Small", "Japan"), + c("Big", "Japan"), c("Mani", "Blanco"), c("Uganda", "Erect"), + c("Mota", "Company")) > names <- MergeKW(names, y1, delim = c("space", "dash", "period")) Warning in gsub(pat, "", x, perl = TRUE) : PCRE pattern compilation error 'invalid range in character class' at '-.]+(?=Dwarf)[[:digit:]]*\b|\b(?<=Gujarat)[\s-.]+(?=Dwarf[[:digit:]]*$)' Error in gsub(pat, "", x, perl = TRUE) : invalid regular expression '(?i)(?<=^Gujarat)[\s-.]+(?=Dwarf)[[:digit:]]*\b|\b(?<=Gujarat)[\s-.]+(?=Dwarf[[:digit:]]*$)' Calls: MergeKW -> sapply -> lapply -> FUN -> gsub Execution halted See: , Version: 0.2.3.3 Check: re-building of vignette outputs, Result: WARNING Error(s) in re-building vignettes: ... --- re-building 'Introduction.Rmd' using rmarkdown_notangle Quitting from lines 327-351 (Introduction.Rmd) Error: processing vignette 'Introduction.Rmd' failed with diagnostics: invalid regular expression '(?i)(?<=^Gujarat)[\s-.]+(?=Dwarf)[[:digit:]]*\b|\b(?<=Gujarat)[\s-.]+(?=Dwarf[[:digit:]]*$)' --- failed re-building 'Introduction.Rmd' SUMMARY: processing the following file failed: 'Introduction.Rmd' Error: Vignette re-building failed. Execution halted See: , Version: 0.2.3.3 Check: whether package can be installed, Result: WARNING Found the following significant warnings: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] See: Version: 0.2.3.3 Check: examples, Result: ERROR Running examples in ‘PGRdup-Ex.R’ failed The error most likely occurred in: > ### Name: MergeKW > ### Title: Merge keyword strings > ### Aliases: MergeKW MergePrefix MergeSuffix > > ### ** Examples > > names <- c("Punjab Bold", "Gujarat- Dwarf", "Nagpur.local", "SAM COL 144", + "SAM COL--280", "NIZAMABAD-LOCAL", "Dark Green Mutant", + "Dixie-Giant", "Georgia- Bunch", "Uganda-erect", "Small Japan", + "Castle Cary", "Punjab erect", "Improved small japan", + "Dark Purple") > > # Merge pairs of strings > y1 <- list(c("Gujarat", "Dwarf"), c("Castle", "Cary"), c("Small", "Japan"), + c("Big", "Japan"), c("Mani", "Blanco"), c("Uganda", "Erect"), + c("Mota", "Company")) > names <- MergeKW(names, y1, delim = c("space", "dash", "period")) Warning in gsub(pat, "", x, perl = TRUE) : PCRE pattern compilation error 'invalid range in character class' at '-.]+(?=Dwarf)[[:digit:]]*\b|\b(?<=Gujarat)[\s-.]+(?=Dwarf[[:digit:]]*$)' Error in gsub(pat, "", x, perl = TRUE) : invalid regular expression '(?i)(?<=^Gujarat)[\s-.]+(?=Dwarf)[[:digit:]]*\b|\b(?<=Gujarat)[\s-.]+(?=Dwarf[[:digit:]]*$)' Calls: MergeKW -> sapply -> lapply -> FUN -> gsub Execution halted See: , Version: 0.2.3.3 Check: re-building of vignette outputs, Result: WARNING Error(s) in re-building vignettes: --- re-building ‘Introduction.Rmd’ using rmarkdown_notangle Quitting from lines 327-351 (Introduction.Rmd) Error: processing vignette 'Introduction.Rmd' failed with diagnostics: invalid regular expression '(?i)(?<=^Gujarat)[\s-.]+(?=Dwarf)[[:digit:]]*\b|\b(?<=Gujarat)[\s-.]+(?=Dwarf[[:digit:]]*$)' --- failed re-building ‘Introduction.Rmd’ SUMMARY: processing the following file failed: ‘Introduction.Rmd’ Error: Vignette re-building failed. Execution halted See: , Version: 0.2.3.3 Check: whether package can be installed, Result: WARNING Found the following significant warnings: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] See: Version: 0.2.3.3 Check: whether package can be installed, Result: WARNING Found the following significant warnings: fdouble_metaphone.c:268:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] See: ,