check for illegal sheetnames

R/WorkbookClass.R

@@ -101,8 +101,8 @@ Workbook$methods(
     vdpi = openxlsx_getOp("vdpi", 300)
   ) {
     if (!missing(sheetName)) {
-      if (grepl(pattern = ":", x = sheetName)) {
-        stop("colon not allowed in sheet names in Excel")
+      if (grepl(pattern = "([/\\\\\\*'?\\[:\\]+])", perl = TRUE, x = sheetName) || nchar(sheetName) == 0) {
+        stop("Illegal character in sheet names. Don't use the following [ ] * / \\\ ? :")
       }
     }
     newSheetIndex <- length(worksheets) + 1L
@@ -219,11 +219,7 @@ Workbook$methods(
 Workbook$methods(
   cloneWorksheet = function(sheetName, clonedSheet) {
     clonedSheet <- validateSheet(clonedSheet)
-    if (!missing(sheetName)) {
-      if (grepl(pattern = ":", x = sheetName)) {
-        stop("colon not allowed in sheet names in Excel")
-      }
-    }
+
     newSheetIndex <- length(worksheets) + 1L
     if (newSheetIndex > 1) {
       sheetId <-
@@ -1116,12 +1112,18 @@ Workbook$methods(
 
 Workbook$methods(
   validateSheet = function(sheetName) {
+    if (!missing(sheetName)) {
+      if (grepl(pattern = "([/\\*'?\\[:\\]+])",perl = T, x = sheetName)) {
+        stop("Illegal character in sheet names. Don't use the following [ ] * / \ ? :")
+      }
+    }
+
     if (!is.numeric(sheetName)) {
       if (is.null(sheet_names)) {
         stop("Workbook does not contain any worksheets.", call. = FALSE)
       }
     }
-
+    
     if (is.numeric(sheetName)) {
       if (sheetName > length(sheet_names)) {
         stop("This Workbook only has ", length(sheet_names),
@@ -1918,12 +1920,15 @@ Workbook$methods(
     if (newSheetName %in% sheet_names) {
       stop(sprintf("Sheet %s already exists!", newSheetName))
     }
-
+
+    if (grepl(pattern = "([/\\*'?\\[:\\]+])",perl = T, x = newSheetName)) {
+      stop("Illegal character in sheet names. Don't use the following [ ] * / \ ? :")
+    }
+
     sheet <- validateSheet(sheet)
 
     oldName <- sheet_names[[sheet]]
     sheet_names[[sheet]] <<- newSheetName
-
     ## Rename in workbook
     sheetId <-
       regmatches(

revdep/README.md

@@ -12,6 +12,7 @@
 |tz       |UTC                          |
 |date     |2021-07-12                   |
 
+
 # Dependencies
 
 |package  |old   |new        |Δ  |
@@ -23,12 +24,15 @@
 
 # Revdeps
 
+
 ## Failed to check (27)
 
+
 |package        |version |error |warning |note |
 |:--------------|:-------|:-----|:-------|:----|
 |appreci8R      |?       |      |        |     |
 |artMS          |?       |      |        |     |
+|cbaf           |?       |      |        |     |
 |CHRONOS        |?       |      |        |     |
 |CNVPanelizer   |?       |      |        |     |
 |DAPAR          |?       |      |        |     |
@@ -49,6 +53,7 @@
 |RIPAT          |?       |      |        |     |
 |sangeranalyseR |1.2.0   |1     |1       |2    |
 |SEtools        |?       |      |        |     |
+|sigFeature     |?       |      |        |     |
 |stplanr        |?       |      |        |     |
 |structToolbox  |?       |      |        |     |
 |TPP            |3.20.0  |1     |        |3    |

revdep/failures.md

@@ -17,6 +17,67 @@
 
 
 
+Error in download.file(url, destfile, method, mode = "wb", ...) : 
+  download from 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz' failed
+In addition: Warning messages:
+1: In download.file(url, destfile, method, mode = "wb", ...) :
+  downloaded length 1562737805 != reported length 1623464748
+2: In download.file(url, destfile, method, mode = "wb", ...) :
+  downloaded length 1562737805 != reported length 1623464748
+3: In download.file(url, destfile, method, mode = "wb", ...) :
+  URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz': Timeout of 60 seconds was reached
+4: In download.file(url, destfile, method, mode = "wb", ...) :
+  URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz': Timeout of 60 seconds was reached
+Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
+  download of package ‘MafDb.1Kgenomes.phase3.hs37d5’ failed
+Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
+  download of package ‘MafDb.1Kgenomes.phase3.hs37d5’ failed
+
+
+```
+### CRAN
+
+```
+
+
+
+Error in download.file(url, destfile, method, mode = "wb", ...) : 
+  download from 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz' failed
+In addition: Warning messages:
+1: In download.file(url, destfile, method, mode = "wb", ...) :
+  downloaded length 1562737805 != reported length 1623464748
+2: In download.file(url, destfile, method, mode = "wb", ...) :
+  downloaded length 1562737805 != reported length 1623464748
+3: In download.file(url, destfile, method, mode = "wb", ...) :
+  URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz': Timeout of 60 seconds was reached
+4: In download.file(url, destfile, method, mode = "wb", ...) :
+  URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz': Timeout of 60 seconds was reached
+Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
+  download of package ‘MafDb.1Kgenomes.phase3.hs37d5’ failed
+Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
+  download of package ‘MafDb.1Kgenomes.phase3.hs37d5’ failed
+
+
+```
+# artMS
+
+<details>
+
+* Version: 
+* GitHub: https://github.com/ycphs/openxlsx
+* Source code: NA
+* Number of recursive dependencies: 0
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+
+
+
 
 
 
@@ -31,7 +92,7 @@
 
 
 ```
-# artMS
+# cbaf
 
 <details>
 
@@ -654,6 +715,7 @@ ERROR: lazy loading failed for package ‘hypeR’
 ```
 # RIPAT
 
+
 <details>
 
 * Version: 
@@ -689,94 +751,69 @@ ERROR: lazy loading failed for package ‘hypeR’
 
 <details>
 
-* Version: 1.2.0
-* GitHub: NA
-* Source code: https://github.com/cran/sangeranalyseR
-* Date/Publication: 2021-05-19
-* Number of recursive dependencies: 142
-
-Run `revdep_details(, "sangeranalyseR")` for more info
+* Version: 
+* GitHub: https://github.com/ycphs/openxlsx
+* Source code: NA
+* Number of recursive dependencies: 0
 
 </details>
 
-## In both
+## Error before installation
 
-*   checking whether package ‘sangeranalyseR’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/sangeranalyseR/new/sangeranalyseR.Rcheck/00install.out’ for details.
-    ```
+### Devel
 
-*   checking for portable file names ... WARNING
-    ```
-    Found the following file with a non-portable file name:
-      docs/wallpaperflare.com_wallpaper (1).jpg
-    These are not fully portable file names.
-    See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
-    ```
+```
 
-*   checking package dependencies ... NOTE
-    ```
-    Depends: includes the non-default packages:
-      'stringr', 'ape', 'Biostrings', 'DECIPHER', 'parallel', 'reshape2',
-      'phangorn', 'sangerseqR', 'gridExtra', 'shiny', 'shinydashboard',
-      'shinyjs', 'data.table', 'plotly', 'DT', 'zeallot', 'excelR',
-      'shinycssloaders', 'ggdendro', 'shinyWidgets', 'openxlsx', 'tools',
-      'rmarkdown', 'kableExtra', 'seqinr', 'BiocStyle', 'logger'
-    Adding so many packages to the search path is excessive and importing
-    selectively is preferable.
-    ```
 
-*   checking for hidden files and directories ... NOTE
-    ```
-    Found the following hidden files and directories:
-      .travis.yml
-      docs/build/html/.buildinfo
-    These were most likely included in error. See section ‘Package
-    structure’ in the ‘Writing R Extensions’ manual.
-    ```
 
-## Installation
+
+
+
+```
+### CRAN
+
+```
+
+
+
+
+
+
+```
+# SEtools
+
+<details>
+
+* Version: 
+* GitHub: https://github.com/ycphs/openxlsx
+* Source code: NA
+* Number of recursive dependencies: 0
+
+</details>
+
+## Error before installation
 
 ### Devel
 
 ```
-* installing *source* package ‘sangeranalyseR’ ...
-** using staged installation
-** R
-** data
-** inst
-** byte-compile and prepare package for lazy loading
-Error: package or namespace load failed for ‘phangorn’ in dyn.load(file, DLLpath = DLLpath, ...):
- unable to load shared object '/home/runner/work/openxlsx/openxlsx/revdep/library/sangeranalyseR/igraph/libs/igraph.so':
-  libglpk.so.40: cannot open shared object file: No such file or directory
-Error: package ‘phangorn’ could not be loaded
-Execution halted
-ERROR: lazy loading failed for package ‘sangeranalyseR’
-* removing ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/sangeranalyseR/new/sangeranalyseR.Rcheck/sangeranalyseR’
+
+
+
+
 
 
 ```
 ### CRAN
 
 ```
-* installing *source* package ‘sangeranalyseR’ ...
-** using staged installation
-** R
-** data
-** inst
-** byte-compile and prepare package for lazy loading
-Error: package or namespace load failed for ‘phangorn’ in dyn.load(file, DLLpath = DLLpath, ...):
- unable to load shared object '/home/runner/work/openxlsx/openxlsx/revdep/library/sangeranalyseR/igraph/libs/igraph.so':
-  libglpk.so.40: cannot open shared object file: No such file or directory
-Error: package ‘phangorn’ could not be loaded
-Execution halted
-ERROR: lazy loading failed for package ‘sangeranalyseR’
-* removing ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/sangeranalyseR/old/sangeranalyseR.Rcheck/sangeranalyseR’
+
+
+
+
 
 
 ```
-# SEtools
+# sigFeature
 
 <details>
 

tests/testthat/test-Worksheet_naming.R

@@ -44,3 +44,29 @@ test_that("Worksheet names", {
   expect_equal(sheetname,names(wb))
   expect_equal("test "A"",wb$sheet_names)
 })
+
+
+test_that("test for illegal characters", {
+  ### 
+
+  wb <- createWorkbook()
+  x <- data.frame(a = 1, b = 2)
+
+  addWorksheet(wb, "Test")
+  for(i in c("[", "]", "*", "/",  "?", ":")){
+    sheetname <- paste0('test_',i)
+    y <- list(a = x, sheetname = x, c = x)
+    expect_error(addWorksheet(wb, sheetname))
+    expect_error(cloneWorksheet(wb, "Test", sheetname))
+    expect_error(renameWorksheet(wb, "Test", sheetname))
+    expect_error(parse(names(wb)<- sheetname))
+    expect_error(parse(buildWorkbook(y, asTable = TRUE)))
+  }
+
+})
+
+
+
+
+
+