Multiple platform build/check report for BioC 3.19 - CHECK results for partCNV on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4758
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4492
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4464
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4464
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for partCNV on kjohnson1

To the developers/maintainers of the partCNV package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/partCNV.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: partCNV

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:partCNV.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings partCNV_1.2.0.tar.gz

StartedAt: 2024-06-18 05:23:11 -0400 (Tue, 18 Jun 2024)

EndedAt: 2024-06-18 05:31:15 -0400 (Tue, 18 Jun 2024)

EllapsedTime: 483.6 seconds

RetCode: 1

Status: ERROR

CheckDir: partCNV.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:partCNV.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings partCNV_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/partCNV.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘partCNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘partCNV’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘partCNV’ 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 ... 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 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
GetCytoLocation: no visible global function definition for ‘data’
GetExprCountCyto: no visible global function definition for ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘partCNV-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GetCytoLocation
> ### Title: Get exact location of the interested cytogenetics feature
> ### Aliases: GetCytoLocation
> 
> ### ** Examples
> 
> ### example 1
> GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)")
downloading 1 resources
retrieving 1 resource
loading from cache
require(“GenomicRanges”)
Interested region: chr20:28100001-51200000.
A total of 381 genes are located in this region.
$chr_location
[1] "chr20"

$cyto_start
[1] 28100001

$cyto_end
[1] 51200000

$overGeneID
  [1] "ENSG00000287889" "ENSG00000205611" "ENSG00000286483" "ENSG00000287288"
  [5] "ENSG00000231934" "ENSG00000215547" "ENSG00000215545" "ENSG00000131068"
  [9] "ENSG00000180483" "ENSG00000204548" "ENSG00000180424" "ENSG00000180383"
 [13] "ENSG00000088320" "ENSG00000233354" "ENSG00000101294" "ENSG00000274364"
 [17] "ENSG00000101898" "ENSG00000235313" "ENSG00000230613" "ENSG00000278276"
 [21] "ENSG00000125968" "ENSG00000131055" "ENSG00000171552" "ENSG00000236559"
 [25] "ENSG00000281376" "ENSG00000088325" "ENSG00000101306" "ENSG00000179772"
 [29] "ENSG00000149599" "ENSG00000131044" "ENSG00000088356" "ENSG00000260903"
 [33] "ENSG00000278012" "ENSG00000226239" "ENSG00000101331" "ENSG00000101336"
 [37] "ENSG00000101337" "ENSG00000275576" "ENSG00000126003" "ENSG00000101346"
 [41] "ENSG00000287850" "ENSG00000101350" "ENSG00000277692" "ENSG00000171456"
 [45] "ENSG00000197183" "ENSG00000236772" "ENSG00000286311" "ENSG00000277301"
 [49] "ENSG00000233293" "ENSG00000204393" "ENSG00000228156" "ENSG00000198547"
 [53] "ENSG00000149600" "ENSG00000088305" "ENSG00000101367" "ENSG00000260536"
 [57] "ENSG00000260257" "ENSG00000215529" "ENSG00000167098" "ENSG00000078898"
 [61] "ENSG00000167104" "ENSG00000186190" "ENSG00000186191" "ENSG00000131050"
 [65] "ENSG00000224876" "ENSG00000131059" "ENSG00000198183" "ENSG00000125999"
 [69] "ENSG00000101391" "ENSG00000101400" "ENSG00000078699" "ENSG00000275223"
 [73] "ENSG00000125967" "ENSG00000149609" "ENSG00000182584" "ENSG00000271803"
 [77] "ENSG00000101412" "ENSG00000101417" "ENSG00000229188" "ENSG00000131061"
 [81] "ENSG00000230753" "ENSG00000101421" "ENSG00000285230" "ENSG00000125970"
 [85] "ENSG00000228386" "ENSG00000125977" "ENSG00000287853" "ENSG00000101440"
 [89] "ENSG00000250917" "ENSG00000101444" "ENSG00000272945" "ENSG00000078747"
 [93] "ENSG00000236388" "ENSG00000231795" "ENSG00000277558" "ENSG00000125971"
 [97] "ENSG00000101460" "ENSG00000101464" "ENSG00000198646" "ENSG00000078804"
[101] "ENSG00000286803" "ENSG00000131067" "ENSG00000131069" "ENSG00000100983"
[105] "ENSG00000078814" "ENSG00000100991" "ENSG00000088298" "ENSG00000101000"
[109] "ENSG00000278367" "ENSG00000126005" "ENSG00000125966" "ENSG00000242372"
[113] "ENSG00000235214" "ENSG00000125998" "ENSG00000101019" "ENSG00000204183"
[117] "ENSG00000125965" "ENSG00000126001" "ENSG00000230155" "ENSG00000125975"
[121] "ENSG00000125991" "ENSG00000061656" "ENSG00000214078" "ENSG00000244462"
[125] "ENSG00000244005" "ENSG00000125995" "ENSG00000131051" "ENSG00000025293"
[129] "ENSG00000171222" "ENSG00000149646" "ENSG00000260032" "ENSG00000234139"
[133] "ENSG00000277235" "ENSG00000237063" "ENSG00000088367" "ENSG00000232406"
[137] "ENSG00000278035" "ENSG00000131043" "ENSG00000080845" "ENSG00000232907"
[141] "ENSG00000101335" "ENSG00000118707" "ENSG00000101084" "ENSG00000101082"
[145] "ENSG00000101079" "ENSG00000149636" "ENSG00000149639" "ENSG00000101342"
[149] "ENSG00000101347" "ENSG00000080839" "ENSG00000269846" "ENSG00000101353"
[153] "ENSG00000118705" "ENSG00000118702" "ENSG00000101363" "ENSG00000286240"
[157] "ENSG00000197122" "ENSG00000166619" "ENSG00000053438" "ENSG00000276603"
[161] "ENSG00000274469" "ENSG00000225759" "ENSG00000204117" "ENSG00000132792"
[165] "ENSG00000132821" "ENSG00000101407" "ENSG00000101413" "ENSG00000277550"
[169] "ENSG00000198959" "ENSG00000149633" "ENSG00000277829" "ENSG00000285347"
[173] "ENSG00000285100" "ENSG00000206249" "ENSG00000101425" "ENSG00000129988"
[177] "ENSG00000275285" "ENSG00000224635" "ENSG00000275401" "ENSG00000196756"
[181] "ENSG00000174365" "ENSG00000170471" "ENSG00000182035" "ENSG00000124143"
[185] "ENSG00000101438" "ENSG00000101442" "ENSG00000101445" "ENSG00000101447"
[189] "ENSG00000274825" "ENSG00000261431" "ENSG00000101452" "ENSG00000277581"
[193] "ENSG00000230324" "ENSG00000287983" "ENSG00000286083" "ENSG00000229976"
[197] "ENSG00000237767" "ENSG00000233415" "ENSG00000223410" "ENSG00000204103"
[201] "ENSG00000229771" "ENSG00000286972" "ENSG00000198900" "ENSG00000226648"
[205] "ENSG00000124181" "ENSG00000174306" "ENSG00000132793" "ENSG00000183798"
[209] "ENSG00000124177" "ENSG00000273951" "ENSG00000225458" "ENSG00000228959"
[213] "ENSG00000196090" "ENSG00000229042" "ENSG00000227599" "ENSG00000233508"
[217] "ENSG00000124193" "ENSG00000185513" "ENSG00000226143" "ENSG00000101049"
[221] "ENSG00000282876" "ENSG00000101052" "ENSG00000101057" "ENSG00000124196"
[225] "ENSG00000233277" "ENSG00000124191" "ENSG00000149596" "ENSG00000287570"
[229] "ENSG00000132823" "ENSG00000223891" "ENSG00000124194" "ENSG00000197296"
[233] "ENSG00000101074" "ENSG00000226812" "ENSG00000101076" "ENSG00000229005"
[237] "ENSG00000233376" "ENSG00000168746" "ENSG00000124120" "ENSG00000132824"
[241] "ENSG00000168734" "ENSG00000196839" "ENSG00000283440" "ENSG00000244558"
[245] "ENSG00000064205" "ENSG00000124249" "ENSG00000276223" "ENSG00000101098"
[249] "ENSG00000286100" "ENSG00000166913" "ENSG00000101104" "ENSG00000025772"
[253] "ENSG00000227477" "ENSG00000101109" "ENSG00000124134" "ENSG00000175121"
[257] "ENSG00000168703" "ENSG00000124102" "ENSG00000124233" "ENSG00000124157"
[261] "ENSG00000124107" "ENSG00000124159" "ENSG00000124232" "ENSG00000124145"
[265] "ENSG00000275894" "ENSG00000204070" "ENSG00000124251" "ENSG00000244274"
[269] "ENSG00000124155" "ENSG00000277022" "ENSG00000101443" "ENSG00000237464"
[273] "ENSG00000101446" "ENSG00000243543" "ENSG00000101448" "ENSG00000158901"
[277] "ENSG00000180205" "ENSG00000180305" "ENSG00000180083" "ENSG00000182931"
[281] "ENSG00000168634" "ENSG00000149651" "ENSG00000124116" "ENSG00000101457"
[285] "ENSG00000175063" "ENSG00000101470" "ENSG00000124104" "ENSG00000101473"
[289] "ENSG00000132801" "ENSG00000168612" "ENSG00000149634" "ENSG00000124257"
[293] "ENSG00000064601" "ENSG00000271984" "ENSG00000100979" "ENSG00000285796"
[297] "ENSG00000100982" "ENSG00000198026" "ENSG00000100985" "ENSG00000204044"
[301] "ENSG00000124140" "ENSG00000124160" "ENSG00000101017" "ENSG00000229957"
[305] "ENSG00000149654" "ENSG00000080189" "ENSG00000273828" "ENSG00000062598"
[309] "ENSG00000198185" "ENSG00000149635" "ENSG00000158296" "ENSG00000273893"
[313] "ENSG00000172315" "ENSG00000271784" "ENSG00000197496" "ENSG00000064655"
[317] "ENSG00000236028" "ENSG00000101040" "ENSG00000267882" "ENSG00000273451"
[321] "ENSG00000231119" "ENSG00000224565" "ENSG00000124151" "ENSG00000196562"
[325] "ENSG00000255438" "ENSG00000234967" "ENSG00000228503" "ENSG00000287443"
[329] "ENSG00000237423" "ENSG00000229522" "ENSG00000286179" "ENSG00000287335"
[333] "ENSG00000276923" "ENSG00000287107" "ENSG00000288083" "ENSG00000286063"
[337] "ENSG00000235621" "ENSG00000236874" "ENSG00000274261" "ENSG00000281365"
[341] "ENSG00000281460" "ENSG00000124126" "ENSG00000286159" "ENSG00000278231"
[345] "ENSG00000124198" "ENSG00000227431" "ENSG00000124207" "ENSG00000124214"
[349] "ENSG00000124228" "ENSG00000124201" "ENSG00000177410" "ENSG00000158445"
[353] "ENSG00000124212" "ENSG00000158470" "ENSG00000197818" "ENSG00000158480"
[357] "ENSG00000124226" "ENSG00000124216" "ENSG00000231265" "ENSG00000244687"
[361] "ENSG00000240849" "ENSG00000237595" "ENSG00000234698" "ENSG00000231742"
[365] "ENSG00000277449" "ENSG00000172216" "ENSG00000224397" "ENSG00000203999"
[369] "ENSG00000233077" "ENSG00000196396" "ENSG00000232043" "ENSG00000042062"
[373] "ENSG00000234693" "ENSG00000124171" "ENSG00000124243" "ENSG00000101126"
[377] "ENSG00000259456" "ENSG00000000419" "ENSG00000124217" "ENSG00000232358"
[381] "ENSG00000026559"

$overGeneName
  [1] "FAM242B"     "LINC01597"   "AL121762.1"  "AL121762.2"  "FAM242A"    
  [6] "DEFB115"     "DEFB116"     "DEFB118"     "DEFB119"     "DEFB121"    
 [11] "DEFB123"     "DEFB124"     "REM1"        "LINC00028"   "HM13"       
 [16] "AL110115.1"  "MCTS2P"      "HM13-IT1"    "HM13-AS1"    "AL110115.2" 
 [21] "ID1"         "COX4I2"      "BCL2L1"      "AL117381.1"  "ABALON"     
 [26] "TPX2"        "MYLK2"       "FOXS1"       "DUSP15"      "TTLL9"      
 [31] "PDRG1"       "XKR7"        "AL031658.2"  "AL031658.1"  "CCM2L"      
 [36] "HCK"         "TM9SF4"      "AL049539.1"  "PLAGL2"      "POFUT1"     
 [41] "AL121897.1"  "KIF3B"       "AL121583.1"  "ASXL1"       "NOL4L"      
 [46] "AL034550.1"  "AL034550.3"  "AL034550.2"  "AL133343.2"  "NOL4L-DT"   
 [51] "AL133343.1"  "C20orf203"   "COMMD7"      "DNMT3B"      "MAPRE1"     
 [56] "AL035071.2"  "AL035071.1"  "EFCAB8"      "SUN5"        "BPIFB2"     
 [61] "BPIFB6"      "BPIFB3"      "BPIFB4"      "BPIFA2"      "AL121901.1" 
 [66] "BPIFA3"      "BPIFA1"      "BPIFB1"      "CDK5RAP1"    "SNTA1"      
 [71] "CBFA2T2"     "AL121906.2"  "NECAB3"      "C20orf144"   "ACTL10"     
 [76] "AL121906.1"  "E2F1"        "PXMP4"       "AL050349.1"  "ZNF341"     
 [81] "ZNF341-AS1"  "CHMP4B"      "RALY-AS1"    "RALY"        "AL031668.1" 
 [86] "EIF2S2"      "AL031668.2"  "ASIP"        "AL035458.2"  "AHCY"       
 [91] "AL356299.2"  "ITCH"        "ITCH-AS1"    "ITCH-IT1"    "AL109923.1" 
 [96] "DYNLRB1"     "MAP1LC3A"    "PIGU"        "NCOA6"       "TP53INP2"   
[101] "AL109824.1"  "GGT7"        "ACSS2"       "GSS"         "MYH7B"      
[106] "TRPC4AP"     "EDEM2"       "PROCR"       "AL356652.1"  "MMP24OS"    
[111] "MMP24"       "EIF6"        "FAM83C-AS1"  "FAM83C"      "UQCC1"      
[116] "GDF5OS"      "GDF5"        "CEP250"      "FO393401.1"  "C20orf173"  
[121] "ERGIC3"      "SPAG4"       "CPNE1"       "RBM12"       "NFS1"       
[126] "ROMO1"       "RBM39"       "PHF20"       "SCAND1"      "CNBD2"      
[131] "NORAD"       "AL035420.1"  "AL035420.3"  "AL035420.2"  "EPB41L1"    
[136] "AL121895.1"  "AL121895.2"  "AAR2"        "DLGAP4"      "DLGAP4-AS1" 
[141] "MYL9"        "TGIF2"       "RAB5IF"      "SLA2"        "NDRG3"      
[146] "DSN1"        "SOGA1"       "TLDC2"       "SAMHD1"      "RBL1"       
[151] "AL136172.1"  "MROH8"       "RPN2"        "GHRH"        "MANBAL"     
[156] "AL034422.1"  "SRC"         "BLCAP"       "NNAT"        "AL109614.1" 
[161] "LINC01746"   "LINC00489"   "AL162293.1"  "CTNNBL1"     "VSTM2L"     
[166] "TTI1"        "RPRD1B"      "AL031651.1"  "TGM2"        "KIAA1755"   
[171] "AL031651.2"  "AL359555.4"  "AL359555.2"  "AL359555.1"  "BPI"        
[176] "LBP"         "AL391095.2"  "AL391095.1"  "AL391095.3"  "SNHG17"     
[181] "SNHG11"      "RALGAPB"     "ADIG"        "ARHGAP40"    "SLC32A1"    
[186] "ACTR5"       "PPP1R16B"    "FAM83D"      "AL023803.2"  "AL023803.1" 
[191] "DHX35"       "AL023803.3"  "LINC01734"   "AL035251.1"  "AL132981.1" 
[196] "AL118523.1"  "LINC01370"   "AL133419.1"  "AL009050.1"  "MAFB"       
[201] "AL035665.1"  "AL035665.2"  "TOP1"        "PLCG1-AS1"   "PLCG1"      
[206] "ZHX3"        "LPIN3"       "EMILIN3"     "CHD6"        "AL031667.3" 
[211] "AL049812.2"  "AL049812.3"  "PTPRT"       "AL031656.1"  "AL031676.1" 
[216] "AL021395.1"  "SRSF6"       "L3MBTL1"     "Z98752.1"    "SGK2"       
[221] "Z98752.4"    "IFT52"       "MYBL2"       "GTSF1L"      "LINC01728"  
[226] "TOX2"        "JPH2"        "AL035447.1"  "OSER1"       "OSER1-DT"   
[231] "GDAP1L1"     "FITM2"       "R3HDML"      "AL117382.1"  "HNF4A"      
[236] "HNF4A-AS1"   "AL117382.2"  "LINC01620"   "TTPAL"       "SERINC3"    
[241] "PKIG"        "ADA"         "LINC01260"   "KCNK15-AS1"  "CCN5"       
[246] "KCNK15"      "AL118522.1"  "RIMS4"       "AL008725.1"  "YWHAB"      
[251] "PABPC1L"     "TOMM34"      "STK4-AS1"    "STK4"        "KCNS1"      
[256] "WFDC5"       "WFDC12"      "PI3"         "SEMG1"       "SEMG2"      
[261] "SLPI"        "MATN4"       "RBPJL"       "SDC4"        "AL021578.1" 
[266] "SYS1"        "TP53TG5"     "DBNDD2"      "PIGT"        "AL031663.3" 
[271] "WFDC2"       "AL031663.2"  "SPINT3"      "WFDC6"       "EPPIN"      
[276] "WFDC8"       "WFDC9"       "WFDC10A"     "WFDC11"      "WFDC10B"    
[281] "WFDC13"      "SPINT4"      "WFDC3"       "DNTTIP1"     "UBE2C"      
[286] "TNNC2"       "SNX21"       "ACOT8"       "ZSWIM3"      "ZSWIM1"     
[291] "SPATA25"     "NEURL2"      "CTSA"        "AL008726.1"  "PLTP"       
[296] "AL162458.1"  "PCIF1"       "ZNF335"      "MMP9"        "SLC12A5-AS1"
[301] "SLC12A5"     "NCOA5"       "CD40"        "AL031687.1"  "CDH22"      
[306] "SLC35C2"     "AL133227.1"  "ELMO2"       "ZNF334"      "OCSTAMP"    
[311] "SLC13A3"     "AL133520.1"  "TP53RK"      "AL031055.1"  "SLC2A10"    
[316] "EYA2"        "AL354766.2"  "ZMYND8"      "AL031666.2"  "AL031666.3" 
[321] "AL031666.1"  "LINC01754"   "NCOA3"       "SULF2"       "AL354813.1" 
[326] "AL357558.2"  "AL357558.1"  "AL357558.3"  "LINC01522"   "LINC01523"  
[331] "AL139351.2"  "AL139351.3"  "AL139351.1"  "AL136102.1"  "AL121888.2" 
[336] "AL121888.1"  "LINC00494"   "AL137078.1"  "AL137078.2"  "AL049541.1" 
[341] "AL049541.2"  "PREX1"       "AL035106.1"  "AL133342.1"  "ARFGEF2"    
[346] "CSE1L-AS1"   "CSE1L"       "STAU1"       "DDX27"       "ZNFX1"      
[351] "ZFAS1"       "KCNB1"       "PTGIS"       "B4GALT5"     "SLC9A8"     
[356] "SPATA2"      "RNF114"      "SNAI1"       "TRERNA1"     "UBE2V1"     
[361] "TMEM189"     "LINC01275"   "AL161937.1"  "LINC01273"   "CEBPB-AS1"  
[366] "CEBPB"       "SMIM25"      "LINC01270"   "LINC01271"   "PTPN1"      
[371] "AL133230.1"  "RIPOR3"      "AL353653.1"  "PARD6B"      "BCAS4"      
[376] "ADNP"        "ADNP-AS1"    "DPM1"        "MOCS3"       "AL050404.1" 
[381] "KCNG1"      

$Downstream_index
[1] 1

> ### example 2
> GetCytoLocation(cyto_feature = "chr20")
loading from cache
Print out all cytogenetics features on chr20:
c(20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 296, 297, 298, 299)c(1, 5100001, 9200001, 12000001, 17900001, 21300001, 22300001, 25700001, 28100001, 30400001, 33500001, 35800001, 39000001, 43100001, 43500001, 47800001, 51200001, 56400001, 57800001, 59700001, 1, 1, 1, 1)c(5100000, 9200000, 12000000, 17900000, 21300000, 22300000, 25700000, 28100000, 30400000, 33500000, 35800000, 39000000, 43100000, 43500000, 47800000, 51200000, 56400000, 57800000, 59700000, 64444167, 128386, 118774, 183433, 58661)c(21, 17, 16, 15, 9, 8, 7, 3, 100, 102, 103, 107, 108, 117, 118, 119, 120, 122, 123, 124, 1, 1, 1, 1)c(2, 6, 2, 6, 2, 4, 2, 1, 1, 2, 4, 2, 6, 2, 4, 2, 6, 2, 5, 2, 2, 2, 2, 2)
$cytogeneticsInfo
                    chr    start      end cytoband     V5
1                 chr20        1  5100000      p13   gneg
2                 chr20  5100001  9200000    p12.3 gpos75
3                 chr20  9200001 12000000    p12.2   gneg
4                 chr20 12000001 17900000    p12.1 gpos75
5                 chr20 17900001 21300000   p11.23   gneg
6                 chr20 21300001 22300000   p11.22 gpos25
7                 chr20 22300001 25700000   p11.21   gneg
8                 chr20 25700001 28100000    p11.1   acen
9                 chr20 28100001 30400000    q11.1   acen
10                chr20 30400001 33500000   q11.21   gneg
11                chr20 33500001 35800000   q11.22 gpos25
12                chr20 35800001 39000000   q11.23   gneg
13                chr20 39000001 43100000      q12 gpos75
14                chr20 43100001 43500000   q13.11   gneg
15                chr20 43500001 47800000   q13.12 gpos25
16                chr20 47800001 51200000   q13.13   gneg
17                chr20 51200001 56400000    q13.2 gpos75
18                chr20 56400001 57800000   q13.31   gneg
19                chr20 57800001 59700000   q13.32 gpos50
20                chr20 59700001 64444167   q13.33   gneg
21 chr20_GL383577v2_alt        1   128386            gneg
22 chr20_KI270869v1_alt        1   118774            gneg
23 chr20_KI270870v1_alt        1   183433            gneg
24 chr20_KI270871v1_alt        1    58661            gneg

$Downstream_index
[1] 0

> ### example 3
> GetCytoLocation(chr = "chr20", start = 25600000, end = 49800000)
downloading 1 resources
retrieving 1 resource
loading from cache
Error: failed to load resource
  name: AH53178
  title: UCSC cytoBand track for hg38
  reason: unknown input format
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. └─partCNV::GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)") at test-partCNVH.R:3:3
    2.   ├─base::data.frame(AnnotationHub()[["AH53178"]])
    3.   ├─AnnotationHub()[["AH53178"]]
    4.   └─AnnotationHub()[["AH53178"]]
    5.     └─AnnotationHub (local) .local(x, i, j = j, ...)
    6.       └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
    7.         └─base::tryCatch(...)
    8.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.               └─value[[3L]](cond)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/partCNV.Rcheck/00check.log’
for details.

Installation output

partCNV.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL partCNV
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘partCNV’ ...
** using staged installation
** R
** data
** 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 (partCNV)

Tests output

partCNV.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(partCNV)
> 
> test_check("partCNV")
loading from cache
loading from cache
loading from cache
loading from cache
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-GetCytoLocation.R:2:3'): GetCytoLocation ───────────────────────
Error: failed to load resource
  name: AH53178
  title: UCSC cytoBand track for hg38
  reason: unknown input format
Backtrace:
     ▆
  1. └─partCNV::GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)") at test-GetCytoLocation.R:2:3
  2.   ├─base::data.frame(AnnotationHub()[["AH53178"]])
  3.   ├─AnnotationHub()[["AH53178"]]
  4.   └─AnnotationHub()[["AH53178"]]
  5.     └─AnnotationHub (local) .local(x, i, j = j, ...)
  6.       └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  7.         └─base::tryCatch(...)
  8.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.               └─value[[3L]](cond)
── Error ('test-GetExprCountCyto.R:3:3'): GetExprCountCyto ─────────────────────
Error: failed to load resource
  name: AH53178
  title: UCSC cytoBand track for hg38
  reason: unknown input format
Backtrace:
     ▆
  1. └─partCNV::GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)") at test-GetExprCountCyto.R:3:3
  2.   ├─base::data.frame(AnnotationHub()[["AH53178"]])
  3.   ├─AnnotationHub()[["AH53178"]]
  4.   └─AnnotationHub()[["AH53178"]]
  5.     └─AnnotationHub (local) .local(x, i, j = j, ...)
  6.       └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  7.         └─base::tryCatch(...)
  8.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.               └─value[[3L]](cond)
── Error ('test-partCNV.R:3:3'): partCNV ───────────────────────────────────────
Error: failed to load resource
  name: AH53178
  title: UCSC cytoBand track for hg38
  reason: unknown input format
Backtrace:
     ▆
  1. └─partCNV::GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)") at test-partCNV.R:3:3
  2.   ├─base::data.frame(AnnotationHub()[["AH53178"]])
  3.   ├─AnnotationHub()[["AH53178"]]
  4.   └─AnnotationHub()[["AH53178"]]
  5.     └─AnnotationHub (local) .local(x, i, j = j, ...)
  6.       └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  7.         └─base::tryCatch(...)
  8.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.               └─value[[3L]](cond)
── Error ('test-partCNVH.R:3:3'): partCNVH ─────────────────────────────────────
Error: failed to load resource
  name: AH53178
  title: UCSC cytoBand track for hg38
  reason: unknown input format
Backtrace:
     ▆
  1. └─partCNV::GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)") at test-partCNVH.R:3:3
  2.   ├─base::data.frame(AnnotationHub()[["AH53178"]])
  3.   ├─AnnotationHub()[["AH53178"]]
  4.   └─AnnotationHub()[["AH53178"]]
  5.     └─AnnotationHub (local) .local(x, i, j = j, ...)
  6.       └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  7.         └─base::tryCatch(...)
  8.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.               └─value[[3L]](cond)

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted

Example timings

partCNV.Rcheck/partCNV-Ex.timings

name

user

system

elapsed