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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiTC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiTC_1.55.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/HiTC.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiTC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTC’ version ‘1.55.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HiTC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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’:
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
  Cannot process chunk/lines:
    BUG FIXES
  Cannot process chunk/lines:
    NEW FEATURES
* 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 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 ... NOTE
directionalityIndex: no visible global function definition for
  ‘subjectHits’
directionalityIndex: no visible global function definition for
  ‘queryHits’
getBlocsIndex: no visible global function definition for ‘Rle’
getExpectedCountsMean: no visible global function definition for ‘Rle’
normLGF: no visible global function definition for ‘glm.nb’
slidingWindow: no visible binding for global variable ‘consV’
splitCombinedContacts : <anonymous>: no visible global function
  definition for ‘seqlevels<-’
divide,HTCexp-HTCexp: no visible global function definition for
  ‘queryHits’
divide,HTCexp-HTCexp: no visible global function definition for
  ‘subjectHits’
isBinned,HTCexp: no visible global function definition for
  ‘countMatches’
substract,HTCexp-HTCexp: no visible global function definition for
  ‘queryHits’
substract,HTCexp-HTCexp: no visible global function definition for
  ‘subjectHits’
Undefined global functions or variables:
  Rle consV countMatches glm.nb queryHits seqlevels<- subjectHits
* checking Rd files ... WARNING
checkRd: (5) HTClist-class.Rd:52-54: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  import.my5C.Rd: Matrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Error: package or namespace load failed for ‘HiTC’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘SparseArray’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Error: package or namespace load failed for ‘HiTC’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘SparseArray’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error: package or namespace load failed for ‘HiTC’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘SparseArray’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
directionalityIndex 8.666  0.138   9.243
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/HiTC.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiTC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘HiTC’ ...
** this is package ‘HiTC’ version ‘1.55.0’
** using staged installation
** R
** data
** 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 (HiTC)