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This page was generated on 2025-10-11 12:03 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
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Package 346/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.43.1  (landing page)
Jianhong Ou
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: devel
git_last_commit: b1cad5f
git_last_commit_date: 2025-07-11 09:55:39 -0400 (Fri, 11 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  

CHECK results for ChIPpeakAnno on nebbiolo2

To the developers/maintainers of the ChIPpeakAnno package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPpeakAnno.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ChIPpeakAnno
Version: 3.43.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ChIPpeakAnno_3.43.1.tar.gz
StartedAt: 2025-10-10 22:21:25 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 22:46:03 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 1478.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ChIPpeakAnno_3.43.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.43.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘ChIPpeakAnno’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 21.1Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    data     12.6Mb
    extdata   7.2Mb
* 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 ... OK
* 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 loading without being on the library search path ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ChIPpeakAnno-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotatePeakInBatch
> ### Title: Obtain the distance to the nearest TSS, miRNA, and/or exon for a
> ###   list of peaks
> ### Aliases: annotatePeakInBatch
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> 
>     ## example 1: annotate myPeakList by TxDb or EnsDb.
>     data(myPeakList)
>     library(ensembldb)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationFilter

Attaching package: 'ensembldb'

The following object is masked from 'package:stats':

    filter

>     library(EnsDb.Hsapiens.v75)
>     annoData <- annoGR(EnsDb.Hsapiens.v75)
Warning in (function (seqlevels, genome, new_style)  :
  cannot switch some GRCh37's seqlevels from NCBI to UCSC style
>     annotatePeak = annotatePeakInBatch(myPeakList[1:6], AnnotationData=annoData)
>     annotatePeak
GRanges object with 6 ranges and 9 metadata columns:
                                seqnames          ranges strand |          peak
                                   <Rle>       <IRanges>  <Rle> |   <character>
   X1_93_556427.ENSG00000223659     chr1   556660-556760      * |  X1_93_556427
   X1_41_559455.ENSG00000223659     chr1   559774-559874      * |  X1_41_559455
   X1_12_703729.ENSG00000240618     chr1   703885-703985      * |  X1_12_703729
   X1_20_925025.ENSG00000272512     chr1   926058-926158      * |  X1_20_925025
  X1_11_1041174.ENSG00000131591     chr1 1041646-1041746      * | X1_11_1041174
  X1_14_1269014.ENSG00000169962     chr1 1270239-1270339      * | X1_14_1269014
                                        feature start_position end_position
                                    <character>      <integer>    <integer>
   X1_93_556427.ENSG00000223659 ENSG00000223659         562757       564390
   X1_41_559455.ENSG00000223659 ENSG00000223659         562757       564390
   X1_12_703729.ENSG00000240618 ENSG00000240618         694412       700305
   X1_20_925025.ENSG00000272512 ENSG00000272512         931346       933431
  X1_11_1041174.ENSG00000131591 ENSG00000131591        1017198      1051741
  X1_14_1269014.ENSG00000169962 ENSG00000169962        1266694      1270686
                                feature_strand insideFeature distancetoFeature
                                   <character>   <character>         <numeric>
   X1_93_556427.ENSG00000223659              -    downstream              7730
   X1_41_559455.ENSG00000223659              -    downstream              4616
   X1_12_703729.ENSG00000240618              -      upstream             -3580
   X1_20_925025.ENSG00000272512              -    downstream              7373
  X1_11_1041174.ENSG00000131591              -        inside             10095
  X1_14_1269014.ENSG00000169962              +        inside              3545
                                shortestDistance fromOverlappingOrNearest
                                       <integer>              <character>
   X1_93_556427.ENSG00000223659             5997          NearestLocation
   X1_41_559455.ENSG00000223659             2883          NearestLocation
   X1_12_703729.ENSG00000240618             3580          NearestLocation
   X1_20_925025.ENSG00000272512             5188          NearestLocation
  X1_11_1041174.ENSG00000131591             9995          NearestLocation
  X1_14_1269014.ENSG00000169962              347          NearestLocation
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths
>     
>     ## example 2: annotate myPeakList (GRanges) 
>     ## with TSS.human.NCBI36 (Granges)
>     data(TSS.human.NCBI36)
>     annotatedPeak = annotatePeakInBatch(myPeakList[1:6], 
+                                         AnnotationData=TSS.human.NCBI36)
>     annotatedPeak
GRanges object with 6 ranges and 9 metadata columns:
                                seqnames          ranges strand |          peak
                                   <Rle>       <IRanges>  <Rle> |   <character>
   X1_93_556427.ENSG00000212875     chr1   556660-556760      * |  X1_93_556427
   X1_41_559455.ENSG00000212678     chr1   559774-559874      * |  X1_41_559455
   X1_12_703729.ENSG00000197049     chr1   703885-703985      * |  X1_12_703729
   X1_20_925025.ENSG00000188290     chr1   926058-926158      * |  X1_20_925025
  X1_11_1041174.ENSG00000131591     chr1 1041646-1041746      * | X1_11_1041174
  X1_14_1269014.ENSG00000107404     chr1 1270239-1270339      * | X1_14_1269014
                                        feature start_position end_position
                                    <character>      <integer>    <integer>
   X1_93_556427.ENSG00000212875 ENSG00000212875         556318       557859
   X1_41_559455.ENSG00000212678 ENSG00000212678         559620       560165
   X1_12_703729.ENSG00000197049 ENSG00000197049         711184       712376
   X1_20_925025.ENSG00000188290 ENSG00000188290         924209       925333
  X1_11_1041174.ENSG00000131591 ENSG00000131591        1007062      1041341
  X1_14_1269014.ENSG00000107404 ENSG00000107404        1260523      1274623
                                feature_strand insideFeature distancetoFeature
                                   <character>   <character>         <numeric>
   X1_93_556427.ENSG00000212875              +        inside               342
   X1_41_559455.ENSG00000212678              +        inside               154
   X1_12_703729.ENSG00000197049              +      upstream             -7299
   X1_20_925025.ENSG00000188290              -      upstream              -725
  X1_11_1041174.ENSG00000131591              -      upstream              -305
  X1_14_1269014.ENSG00000107404              -        inside              4384
                                shortestDistance fromOverlappingOrNearest
                                       <integer>              <character>
   X1_93_556427.ENSG00000212875              342          NearestLocation
   X1_41_559455.ENSG00000212678              154          NearestLocation
   X1_12_703729.ENSG00000197049             7199          NearestLocation
   X1_20_925025.ENSG00000188290              725          NearestLocation
  X1_11_1041174.ENSG00000131591              305          NearestLocation
  X1_14_1269014.ENSG00000107404             4284          NearestLocation
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths
>     
>     ## example 3: you have a list of transcription factor biding sites from 
>     ## literature and are interested in determining the extent of the overlap 
>     ## to the list of peaks from your experiment. Prior calling the function 
>     ## annotatePeakInBatch, need to represent both dataset as GRanges 
>     ## where start is the start of the binding site, end is the end of the 
>     ## binding site, names is the name of the binding site, space and strand 
>     ## are the chromosome name and strand where the binding site is located.
>     
>     myexp <- GRanges(seqnames=c(6,6,6,6,5,4,4), 
+                      IRanges(start=c(1543200,1557200,1563000,1569800,
+                                      167889600,100,1000),
+                              end=c(1555199,1560599,1565199,1573799,
+                                    167893599,200,1200),
+                              names=c("p1","p2","p3","p4","p5","p6", "p7")), 
+                      strand="+")
>     literature <- GRanges(seqnames=c(6,6,6,6,5,4,4), 
+                           IRanges(start=c(1549800,1554400,1565000,1569400,
+                                           167888600,120,800),
+                                   end=c(1550599,1560799,1565399,1571199,
+                                         167888999,140,1400),
+                                   names=c("f1","f2","f3","f4","f5","f6","f7")),
+                           strand=rep(c("+", "-"), c(5, 2)))
>     annotatedPeak1 <- annotatePeakInBatch(myexp, 
+                                           AnnotationData=literature)
>     pie(table(annotatedPeak1$insideFeature))
>     annotatedPeak1
GRanges object with 7 ranges and 9 metadata columns:
        seqnames              ranges strand |        peak     feature
           <Rle>           <IRanges>  <Rle> | <character> <character>
  p1.f1        6     1543200-1555199      + |          p1          f1
  p2.f2        6     1557200-1560599      + |          p2          f2
  p3.f3        6     1563000-1565199      + |          p3          f3
  p4.f4        6     1569800-1573799      + |          p4          f4
  p5.f5        5 167889600-167893599      + |          p5          f5
  p6.f6        4             100-200      + |          p6          f6
  p7.f7        4           1000-1200      + |          p7          f7
        start_position end_position feature_strand  insideFeature
             <integer>    <integer>    <character>    <character>
  p1.f1        1549800      1550599              + includeFeature
  p2.f2        1554400      1560799              +         inside
  p3.f3        1565000      1565399              +   overlapStart
  p4.f4        1569400      1571199              +     overlapEnd
  p5.f5      167888600    167888999              +     downstream
  p6.f6            120          140              - includeFeature
  p7.f7            800         1400              -         inside
        distancetoFeature shortestDistance fromOverlappingOrNearest
                <numeric>        <integer>              <character>
  p1.f1             -6600             4600          NearestLocation
  p2.f2              2800              200          NearestLocation
  p3.f3             -2000              199          NearestLocation
  p4.f4               400              400          NearestLocation
  p5.f5              1000              601          NearestLocation
  p6.f6                40               20          NearestLocation
  p7.f7               400              200          NearestLocation
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths
>     ### use toGRanges or rtracklayer::import to convert BED or GFF format
>     ###  to GRanges before calling annotatePeakInBatch
>     test.bed <- data.frame(space=c("4", "6"), 
+                            start=c("100", "1000"),
+                            end=c("200", "1100"), 
+                            name=c("peak1", "peak2"))
>     test.GR = toGRanges(test.bed)
>     annotatePeakInBatch(test.GR, AnnotationData = literature)
GRanges object with 2 ranges and 9 metadata columns:
           seqnames    ranges strand |        peak     feature start_position
              <Rle> <IRanges>  <Rle> | <character> <character>      <integer>
  peak1.f6        4   100-200      * |       peak1          f6            120
  peak2.f1        6 1000-1100      * |       peak2          f1        1549800
           end_position feature_strand  insideFeature distancetoFeature
              <integer>    <character>    <character>         <numeric>
  peak1.f6          140              - includeFeature                40
  peak2.f1      1550599              +       upstream          -1548800
           shortestDistance fromOverlappingOrNearest
                  <integer>              <character>
  peak1.f6               20          NearestLocation
  peak2.f1          1548700          NearestLocation
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
>  
>  library(testthat)

Attaching package: 'testthat'

The following object is masked from 'package:AnnotationFilter':

    not

>   peak <- GRanges(seqnames = "chr1", 
+                   IRanges(start = 24736757, end=24737528,
+                           names = "testPeak"))
>   data(TSS.human.GRCh37)
>   TSS.human.GRCh37[names(TSS.human.GRCh37)== "ENSG00000001461"]
GRanges object with 1 range and 1 metadata column:
                  seqnames            ranges strand |            description
                     <Rle>         <IRanges>  <Rle> |            <character>
  ENSG00000001461        1 24742285-24799466      + | NIPA-like domain con..
  -------
  seqinfo: 72 sequences from an unspecified genome; no seqlengths
>   # GRanges object with 1 range and 1 metadata column:
>   # seqnames            ranges strand |            description
>   #<Rle>         <IRanges>  <Rle> |            <character>
>   # ENSG00000001461        1 24742285-24799466      + | NIPA-like domain con..
>   peak
GRanges object with 1 range and 0 metadata columns:
           seqnames            ranges strand
              <Rle>         <IRanges>  <Rle>
  testPeak     chr1 24736757-24737528      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
>   #GRanges object with 1 range and 0 metadata columns:
>   #   seqnames            ranges strand
>   #<Rle>         <IRanges>  <Rle>
>   #  testPeak     chr1 24736757-24737528      *
>   TSS.human.GRCh37[names(TSS.human.GRCh37)== "ENSG00000001460"]
GRanges object with 1 range and 1 metadata column:
                  seqnames            ranges strand |            description
                     <Rle>         <IRanges>  <Rle> |            <character>
  ENSG00000001460        1 24683490-24743424      - | UPF0490 protein C1or..
  -------
  seqinfo: 72 sequences from an unspecified genome; no seqlengths
>   #GRanges object with 1 range and 1 metadata column:
>   #   seqnames            ranges strand |            description
>   #<Rle>         <IRanges>  <Rle> |            <character>
>   #   ENSG00000001460        1 24683490-24743424      - | UPF0490 protein C1or..
>   ap <- annotatePeakInBatch(peak, Annotation=TSS.human.GRCh37, 
+                             PeakLocForDistance = "start")
>   stopifnot(ap$feature=="ENSG00000001461")
>   ap <- annotatePeakInBatch(peak, Annotation=TSS.human.GRCh37,
+                             PeakLocForDistance = "end")
>   stopifnot(ap$feature=="ENSG00000001461")
>   ap <- annotatePeakInBatch(peak, Annotation=TSS.human.GRCh37,
+                             PeakLocForDistance = "middle")
>   stopifnot(ap$feature=="ENSG00000001461")
>   ap <- annotatePeakInBatch(peak, Annotation=TSS.human.GRCh37,
+                             PeakLocForDistance = "endMinusStart")
>   stopifnot(ap$feature=="ENSG00000001461")
>   ## Let's calculate the distances between the peak and the TSS of the genes
>   ## in the annotation file used for annotating the peaks.
>   ## Please note that we need to compute the distance using the annotation
>   ## file TSS.human.GRCh37.
>   ## If you would like to use  TxDb.Hsapiens.UCSC.hg19.knownGene, 
>   ## then you will need to annotate the peaks
>   ## using TxDb.Hsapiens.UCSC.hg19.knownGene as well.
>   ### using start
>   start(peak) -start(TSS.human.GRCh37[names(TSS.human.GRCh37)== 
+                                       "ENSG00000001461"]) #picked
[1] -5528
>   #[1] -5528
>   start(peak) -end(TSS.human.GRCh37[names(TSS.human.GRCh37)==
+                                    "ENSG00000001460"])
[1] -6667
>   #[1] -6667
>   #### using middle
>   (start(peak) + end(peak))/2 -
+       start(TSS.human.GRCh37[names(TSS.human.GRCh37)== "ENSG00000001461"])
[1] -5142.5
>   #[1] -5142.5
>   (start(peak) + end(peak))/2 -
+       end(TSS.human.GRCh37[names(TSS.human.GRCh37)== "ENSG00000001460"])
[1] -6281.5
>   # [1] 49480566
>   end(peak) -start(TSS.human.GRCh37[names(TSS.human.GRCh37)==
+                                    "ENSG00000001461"]) #picked
[1] -4757
>   # [1] -4757
>   end(peak) -end(TSS.human.GRCh37[names(TSS.human.GRCh37)==
+                                  "ENSG00000001460"])
[1] -5896
>   # [1] -5896
>   #### using endMinusStart
>   end(peak) - start(TSS.human.GRCh37[names(TSS.human.GRCh37)==
+                                     "ENSG00000001461"]) ## picked
[1] -4757
>   # [1] -4575
>   start(peak) -end(TSS.human.GRCh37[names(TSS.human.GRCh37)==
+                                     "ENSG00000001460"])
[1] -6667
>   #[1] -6667
>   ###### using txdb object to annotate the peaks
>   library(org.Hs.eg.db)
>   select(org.Hs.eg.db, key="STPG1", keytype="SYMBOL",
+          columns=c("ENSEMBL", "ENTREZID", "SYMBOL"))
'select()' returned 1:1 mapping between keys and columns
  SYMBOL         ENSEMBL ENTREZID
1  STPG1 ENSG00000001460    90529
>   #  SYMBOL         ENSEMBL ENTREZID
>   #  STPG1 ENSG00000001460    90529
>   select(org.Hs.eg.db, key= "ENSG00000001461", keytype="ENSEMBL",
+          columns=c("ENSEMBL", "ENTREZID", "SYMBOL"))
'select()' returned 1:1 mapping between keys and columns
          ENSEMBL ENTREZID SYMBOL
1 ENSG00000001461    57185 NIPAL3
>   #ENSEMBL ENTREZID SYMBOL
>   # ENSG00000001461    57185 NIPAL3
>   require(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
>   txdb.ann <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
  24 genes were dropped because they have exons located on both strands of the
  same reference sequence or on more than one reference sequence, so cannot be
  represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
  object, or use suppressMessages() to suppress this message.
>   STPG1 <- select(org.Hs.eg.db, key="STPG1", keytype="SYMBOL",
+                   columns=c( "SYMBOL", "ENSEMBL", "ENTREZID"))[1,3]
'select()' returned 1:1 mapping between keys and columns
>   NIPAL3 <- select(org.Hs.eg.db, key="NIPAL3", keytype="SYMBOL",
+                    columns=c( "SYMBOL", "ENSEMBL", "ENTREZID"))[1,3]
'select()' returned 1:1 mapping between keys and columns
>   ap <- annotatePeakInBatch(peak, Annotation=txdb.ann,
+                             PeakLocForDistance = "start")
>   expect_equal(ap$feature, STPG1)
Error: ap$feature not equal to `STPG1`.
1/1 mismatches
x[1]: "57185"
y[1]: "90529"
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.

Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ChIPpeakAnno’ ...
** this is package ‘ChIPpeakAnno’ version ‘3.43.1’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (ChIPpeakAnno)

Tests output

ChIPpeakAnno.Rcheck/tests/runTests.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("ChIPpeakAnno") || stop("unable to load Package:ChIPpeakAnno")
Loading required package: ChIPpeakAnno
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: GenomicRanges
Loading required package: Seqinfo
[1] TRUE
> require("BSgenome.Drerio.UCSC.danRer7") || stop("unable to load Package:BSgenome.Drerio.UCSC.danRer7")
Loading required package: BSgenome.Drerio.UCSC.danRer7
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer
[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg19") || stop("unable to load Package:BSgenome.Hsapiens.UCSC.hg19")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
[1] TRUE
> require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db")
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


[1] TRUE
> require("org.Ce.eg.db") || stop("unable to load Package:org.Ce.eg.db")
Loading required package: org.Ce.eg.db

[1] TRUE
> require("BSgenome.Celegans.UCSC.ce10") || stop("unable to load Package:BSgenome.Celegans.UCSC.ce10")
Loading required package: BSgenome.Celegans.UCSC.ce10
[1] TRUE
> require("EnsDb.Hsapiens.v79") || stop("unable to load Package:EnsDb.Hsapiens.v79")
Loading required package: EnsDb.Hsapiens.v79
Loading required package: ensembldb
Loading required package: GenomicFeatures
Loading required package: AnnotationFilter

Attaching package: 'ensembldb'

The following object is masked from 'package:stats':

    filter

[1] TRUE
> require("TxDb.Hsapiens.UCSC.hg38.knownGene") || stop("unable to load TxDb.Hsapiens.UCSC.hg38.knownGene")
Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene
[1] TRUE
> require("biomaRt") || stop("unable to load biomaRt")
Loading required package: biomaRt
[1] TRUE
> require("reactome.db") || stop("unable to load reactome.db")
Loading required package: reactome.db
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat

Attaching package: 'testthat'

The following object is masked from 'package:AnnotationFilter':

    not

[1] TRUE
> test_check("ChIPpeakAnno")
INFO [2025-10-10 22:30:39] $cat.cex
INFO [2025-10-10 22:30:39] [1] 1
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $cat.col
INFO [2025-10-10 22:30:39] [1] "black"
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $cat.fontface
INFO [2025-10-10 22:30:39] [1] "plain"
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $cat.fontfamily
INFO [2025-10-10 22:30:39] [1] "serif"
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $x
INFO [2025-10-10 22:30:39] $x$TF1
INFO [2025-10-10 22:30:39] [1] 3 4 5
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $x$TF2
INFO [2025-10-10 22:30:39] [1] 1 2 3 4 5
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $disable.logging
INFO [2025-10-10 22:30:39] [1] TRUE
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $filename
INFO [2025-10-10 22:30:39] NULL
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $cat.cex
INFO [2025-10-10 22:30:39] [1] 1
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $cat.col
INFO [2025-10-10 22:30:39] [1] "black"
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $cat.fontface
INFO [2025-10-10 22:30:39] [1] "plain"
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $cat.fontfamily
INFO [2025-10-10 22:30:39] [1] "serif"
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $x
INFO [2025-10-10 22:30:39] $x$TF1
INFO [2025-10-10 22:30:39] [1] 3 4 5
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $x$TF2
INFO [2025-10-10 22:30:39] [1] 1 2 4 5
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $x$TF3
INFO [2025-10-10 22:30:39] [1] 3 4 5
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $x$TF4
INFO [2025-10-10 22:30:39] [1] 1 2 4 5
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $disable.logging
INFO [2025-10-10 22:30:39] [1] TRUE
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:39] $filename
INFO [2025-10-10 22:30:39] NULL
INFO [2025-10-10 22:30:39] 
INFO [2025-10-10 22:30:40] $scaled
INFO [2025-10-10 22:30:40] [1] FALSE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $euler.d
INFO [2025-10-10 22:30:40] [1] FALSE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.cex
INFO [2025-10-10 22:30:40] [1] 1
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.col
INFO [2025-10-10 22:30:40] [1] "black"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.fontface
INFO [2025-10-10 22:30:40] [1] "plain"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.fontfamily
INFO [2025-10-10 22:30:40] [1] "serif"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $x
INFO [2025-10-10 22:30:40] $x$TF1
INFO [2025-10-10 22:30:40] [1] 1 2 3
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $x$TF2
INFO [2025-10-10 22:30:40] [1] 1 2 3
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $disable.logging
INFO [2025-10-10 22:30:40] [1] TRUE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $filename
INFO [2025-10-10 22:30:40] NULL
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $scaled
INFO [2025-10-10 22:30:40] [1] FALSE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $euler.d
INFO [2025-10-10 22:30:40] [1] FALSE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.cex
INFO [2025-10-10 22:30:40] [1] 1
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.col
INFO [2025-10-10 22:30:40] [1] "black"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.fontface
INFO [2025-10-10 22:30:40] [1] "plain"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.fontfamily
INFO [2025-10-10 22:30:40] [1] "serif"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $x
INFO [2025-10-10 22:30:40] $x$TF1
INFO [2025-10-10 22:30:40] [1] 4 5 6
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $x$TF2
INFO [2025-10-10 22:30:40] [1] 1 2 3
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $disable.logging
INFO [2025-10-10 22:30:40] [1] TRUE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $filename
INFO [2025-10-10 22:30:40] NULL
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $scaled
INFO [2025-10-10 22:30:40] [1] FALSE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $euler.d
INFO [2025-10-10 22:30:40] [1] FALSE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.cex
INFO [2025-10-10 22:30:40] [1] 1
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.col
INFO [2025-10-10 22:30:40] [1] "black"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.fontface
INFO [2025-10-10 22:30:40] [1] "plain"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.fontfamily
INFO [2025-10-10 22:30:40] [1] "serif"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $x
INFO [2025-10-10 22:30:40] $x$TF1
INFO [2025-10-10 22:30:40] [1] 4 5 6
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $x$TF2
INFO [2025-10-10 22:30:40] [1] 1 2 3
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $disable.logging
INFO [2025-10-10 22:30:40] [1] TRUE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $filename
INFO [2025-10-10 22:30:40] NULL
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $scaled
INFO [2025-10-10 22:30:40] [1] FALSE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $euler.d
INFO [2025-10-10 22:30:40] [1] FALSE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.cex
INFO [2025-10-10 22:30:40] [1] 1
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.col
INFO [2025-10-10 22:30:40] [1] "black"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.fontface
INFO [2025-10-10 22:30:40] [1] "plain"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $cat.fontfamily
INFO [2025-10-10 22:30:40] [1] "serif"
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $x
INFO [2025-10-10 22:30:40] $x$TF1
INFO [2025-10-10 22:30:40] [1] 4 5 6
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $x$TF2
INFO [2025-10-10 22:30:40] [1] 1 2 3
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $x$TF3
INFO [2025-10-10 22:30:40] [1] 2 3 6
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $disable.logging
INFO [2025-10-10 22:30:40] [1] TRUE
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:40] $filename
INFO [2025-10-10 22:30:40] NULL
INFO [2025-10-10 22:30:40] 
INFO [2025-10-10 22:30:41] $scaled
INFO [2025-10-10 22:30:41] [1] FALSE
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $euler.d
INFO [2025-10-10 22:30:41] [1] FALSE
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $cat.cex
INFO [2025-10-10 22:30:41] [1] 1
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $cat.col
INFO [2025-10-10 22:30:41] [1] "black"
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $cat.fontface
INFO [2025-10-10 22:30:41] [1] "plain"
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $cat.fontfamily
INFO [2025-10-10 22:30:41] [1] "serif"
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $x
INFO [2025-10-10 22:30:41] $x$TF1
INFO [2025-10-10 22:30:41] [1] 3 4 5
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $x$TF2
INFO [2025-10-10 22:30:41] [1] 1 2 5
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $x$TF3
INFO [2025-10-10 22:30:41] [1] 1 2 5
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $disable.logging
INFO [2025-10-10 22:30:41] [1] TRUE
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $filename
INFO [2025-10-10 22:30:41] NULL
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $scaled
INFO [2025-10-10 22:30:41] [1] FALSE
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $euler.d
INFO [2025-10-10 22:30:41] [1] FALSE
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $cat.cex
INFO [2025-10-10 22:30:41] [1] 1
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $cat.col
INFO [2025-10-10 22:30:41] [1] "black"
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $cat.fontface
INFO [2025-10-10 22:30:41] [1] "plain"
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $cat.fontfamily
INFO [2025-10-10 22:30:41] [1] "serif"
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $x
INFO [2025-10-10 22:30:41] $x$TF1
INFO [2025-10-10 22:30:41] [1] 3 4 5
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $x$TF2
INFO [2025-10-10 22:30:41] [1] 1 2 5
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $x$TF3
INFO [2025-10-10 22:30:41] [1] 1 2 5
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $x$TF4
INFO [2025-10-10 22:30:41] [1] 1 2 5
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $disable.logging
INFO [2025-10-10 22:30:41] [1] TRUE
INFO [2025-10-10 22:30:41] 
INFO [2025-10-10 22:30:41] $filename
INFO [2025-10-10 22:30:41] NULL
INFO [2025-10-10 22:30:41] 
[ FAIL 0 | WARN 2 | SKIP 6 | PASS 324 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• empty test (6): 'test_binOverGene.R:1:1', 'test_binOverRegions.R:1:1',
  'test_enrichmentPlot.R:1:1', 'test_getAnnotation.R:1:1',
  'test_reCenterPeaks.R:1:1', 'test_write2FASTA.R:1:1'

[ FAIL 0 | WARN 2 | SKIP 6 | PASS 324 ]
> 
> proc.time()
   user  system elapsed 
175.434   4.281 180.800

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0000.000
ExonPlusUtr.human.GRCh373.4750.1693.644
HOT.spots0.1340.0230.157
IDRfilter0.0000.0000.001
Peaks.Ste12.Replicate10.0470.0020.050
Peaks.Ste12.Replicate20.0100.0010.012
Peaks.Ste12.Replicate30.0110.0000.011
TSS.human.GRCh370.1050.0050.110
TSS.human.GRCh380.2150.0050.220
TSS.human.NCBI360.1050.0060.110
TSS.mouse.GRCm380.0930.0120.105
TSS.mouse.NCBIM370.0860.0090.095
TSS.rat.RGSC3.40.0760.0050.081
TSS.rat.Rnor_5.00.0640.0060.070
TSS.zebrafish.Zv80.0670.0080.075
TSS.zebrafish.Zv90.0860.0080.094
addAncestors0.9080.0350.943
addGeneIDs0.7440.0250.770
addMetadata1.2840.0931.377
annoGR000
annoPeaks2.5270.2282.756