| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:33 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
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To the developers/maintainers of the ToxicoGx package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ToxicoGx.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2052/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ToxicoGx 2.3.0 (landing page) Benjamin Haibe-Kains
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: ToxicoGx |
| Version: 2.3.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ToxicoGx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ToxicoGx_2.3.0.tar.gz |
| StartedAt: 2023-02-07 17:48:51 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 17:53:51 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 300.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ToxicoGx.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ToxicoGx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ToxicoGx_2.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ToxicoGx.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ToxicoGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ToxicoGx’ version ‘2.3.0’
* 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 ‘ToxicoGx’ 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 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 dependencies in R code ... NOTE
':::' call which should be '::': ‘CoreGx:::updateSampleId’
See the note in ?`:::` about the use of this operator.
Missing object imported by a ':::' call: ‘CoreGx:::updateTreamentId’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
computeLimmaDiffExpr,ToxicoSet: no visible global function definition
for ‘metadata<-’
computeLimmaDiffExpr,ToxicoSet: no visible binding for global variable
‘cell’
Undefined global functions or variables:
cell metadata<-
* 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 ... NOTE
Note: found 47 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ToxicoGx-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ToxicoSet-accessors
> ### Title: Accessing and modifying information in a 'CoreSet'
> ### Aliases: ToxicoSet-accessors drugInfo treatmentInfo,ToxicoSet-method
> ### treatmentInfo drugInfo<- treatmentInfo<-,ToxicoSet,data.frame-method
> ### treatmentInfo<- drugNames treatmentNames,ToxicoSet-method
> ### treatmentNames drugNames<-
> ### treatmentNames<-,ToxicoSet,character-method treatmentNames<-
> ### annotation,ToxicoSet-method annotation
> ### annotation<-,ToxicoSet,list-method annotation<-
> ### dateCreated,ToxicoSet-method dateCreated
> ### dateCreated<-,ToxicoSet,character-method
> ### dateCreated<-,ToxicoSet-method dateCreated<- name,ToxicoSet-method
> ### name name<-,ToxicoSet-method name<-,ToxicoSet,character-method name<-
> ### sampleInfo,ToxicoSet-method sampleInfo cellInfo,ToxicoSet-method
> ### cellInfo sampleInfo<-,ToxicoSet,data.frame-method sampleInfo<-
> ### cellInfo<-,ToxicoSet,data.frame-method cellInfo<-
> ### sampleNames,ToxicoSet-method sampleName,ToxicoSet-method sampleNames
> ### cellName,ToxicoSet-method cellNames
> ### sampleNames<-,ToxicoSet,character-method
> ### sampleNames<-,ToxicoSet,list-method sampleNames<-
> ### cellNames<-,ToxicoSet,list-method cellNames<-
> ### curation,ToxicoSet-method curation curation<-,ToxicoSet,list-method
> ### curation<- datasetType,ToxicoSet-method datasetType
> ### datasetType<-,ToxicoSet,character-method datasetType<-
> ### molecularProfiles,ToxicoSet-method molecularProfiles
> ### molecularProfiles<-,ToxicoSet,character,character,matrix-method
> ### molecularProfiles<-,ToxicoSet,character,missing,matrix-method
> ### molecularProfiles<-,ToxicoSet,missing,missing,list-method
> ### molecularProfiles<-,ToxicoSet,missing,missing,MutliAssayExperiment-method
> ### molecularProfiles<- featureInfo,ToxicoSet-method featureInfo
> ### featureInfo<-,ToxicoSet,character,data.frame-method
> ### featureInfo<-,ToxicoSet,character,DataFrame-method featureInfo<-
> ### phenoInfo,ToxicoSet,character-method phenoInfo
> ### phenoInfo<-,ToxicoSet,character,data.frame-method
> ### phenoInfo<-,ToxicoSet,character,DataFrame-method phenoInfo<-
> ### fNames,ToxicoSet,character-method fNames
> ### fNames<-,ToxicoSet,character,character-method fNames<-
> ### mDataNames,ToxicoSet-method mDataNames mDataNames<-,ToxicoSet-method
> ### mDataNames<-,ToxicoSet,ANY-method mDataNames<-
> ### molecularProfilesSlot,ToxicoSet-method
> ### moleculerProfilesSlot,ToxicoSet-method molecularProfilesSlot
> ### molecularProfilesSlot<-,ToxicoSet,list_OR_MAE-method
> ### molecularProfilesSlot<-,ToxicoSet,list-method
> ### molecularProfilesSlot<-ToxicoSet,MultiAssayExperiment-method
> ### molecularProfilesSlot<- sensitivityInfo,ToxicoSet-method
> ### sensitivityInfo,ToxicoSet,missing-method
> ### sensitivityInfo,ToxicoSet,character-method
> ### sensitivityInfo<-,ToxicoSet,data.frame-method
> ### sensitivityInfo<-,ToxicoSet,missing,data.frame-method
> ### sensitvityInfo<-,ToxicoSet,character,data.frame-method
> ### sensitivityMeasures,ToxicoSet-method
> ### sensitivityMeasures<-,ToxicoSet,character-method
> ### sensitivityProfiles,ToxicoSet-method
> ### sensitivityProfiles<-,ToxicoSet,data.frame-method
> ### sensitivityRaw,ToxicoSet-method
> ### sensitivityRaw<-,ToxicoSet,array-method
> ### treatmentResponse,ToxicoSet-method treatmentResponse sensitivitySlot
> ### treatmentResponse<-,ToxicoSet,list_OR_LongTable-method
> ### treatmentResponse<- treamentResponse<-,ToxicoSet,list-method
> ### treatmentResponse<-,ToxicoSet,LongTable-method sensitivitySlot<-
> ### sensNumber,ToxicoSet-method sensNumber
> ### sensNumber<-,ToxicoSet,matrix-method sensNumber<-
> ### pertNumber,ToxicoSet-method pertNumber
> ### pertNumber<-,ToxicoSet,array-method pertNumber<-
>
> ### ** Examples
>
> data(TGGATESsmall)
> treatmentInfo(TGGATESsmall)
treatmentid
1-Naphthyl isothiocyanate 1-Naphthyl isothiocyanate
Phenylbutazone Phenylbutazone
Rifampicin Rifampicin
Indomethacin Indomethacin
Chlorpromazine Chlorpromazine
Isoniazid Isoniazid
Acetaminophen Acetaminophen
Clofibrate Clofibrate
Carbon tetrachloride Carbon tetrachloride
Phenobarbital Phenobarbital
Methapyrilene Methapyrilene
Ethionine Ethionine
Carbamazepine Carbamazepine
Cimetidine Cimetidine
Fluphenazine Fluphenazine
Pirinixic acid Pirinixic acid
Aspirin Aspirin
Gemfibrozil Gemfibrozil
Labetalol Labetalol
Hexachlorobenzene Hexachlorobenzene
Amiodarone Amiodarone
Allopurinol Allopurinol
Benzbromarone Benzbromarone
Nitrofurantoin Nitrofurantoin
Diazepam Diazepam
Griseofulvin Griseofulvin
Sulfasalazine Sulfasalazine
Bromobenzene Bromobenzene
Cyclophosphamide Cyclophosphamide
Omeprazole Omeprazole
Allyl alcohol Allyl alcohol
Valproic acid Valproic acid
Diclofenac Diclofenac
Propylthiouracil Propylthiouracil
2H-1-Benzopyran-2-one 2H-1-Benzopyran-2-one
Haloperidol Haloperidol
Tetracycline Tetracycline
Flutamide Flutamide
Glyburide Glyburide
Azathioprine Azathioprine
Perhexiline Perhexiline
Phenytoin Phenytoin
Doxepin Hydrochloride Doxepin Hydrochloride
Thioridazine Thioridazine
Methyltestosterone Methyltestosterone
Lomustine Lomustine
Thioacetamide Thioacetamide
Xolegel Xolegel
Ciprofloxacin Ciprofloxacin
Pemoline Pemoline
Chlormezanone Chlormezanone
Metformin Metformin
Tamoxifen Tamoxifen
Ethinyl estradiol Ethinyl estradiol
Methyldopa Methyldopa
Methimazole Methimazole
Monocrotaline Monocrotaline
Retinol Retinol
Quinidine Quinidine
Tacrine Tacrine
Moxisylyte Moxisylyte
Iproniazid Iproniazid
Chloramphenicol Chloramphenicol
Nitrofurazone Nitrofurazone
Trimipramine Trimipramine
Amitriptyline Amitriptyline
Hydroxyzine Hydroxyzine
2-(4-Isobutylphenyl)propanoic acid 2-(4-Isobutylphenyl)propanoic acid
Naproxen Naproxen
Furosemide Furosemide
Fenofibrate Fenofibrate
Chlorpropamide Chlorpropamide
Nicotinic acid Nicotinic acid
Erythromycin ethylsuccinate Erythromycin ethylsuccinate
Ethambutol Ethambutol
Mefenamic acid Mefenamic acid
Pepcid Pepcid
Ranitidine Ranitidine
Tannic acid Tannic acid
Captopril Captopril
Caffeine Caffeine
Papaverine Papaverine
Enalapril Enalapril
Theophylline Theophylline
Sulindac Sulindac
D-Penicillamine D-Penicillamine
Disopyramide Disopyramide
Mexiletine Mexiletine
Acetazolamide Acetazolamide
Disulfiram Disulfiram
Colchicine Colchicine
Nifedipine Nifedipine
Diltiazem Diltiazem
Chlorpheniramine Chlorpheniramine
Tolbutamide Tolbutamide
Acarbose Acarbose
Simvastatin Simvastatin
Meloxicam Meloxicam
Chlormadinone Chlormadinone
Benziodarone Benziodarone
Ethionamide Ethionamide
Nimesulide Nimesulide
Ethanol Ethanol
Bucetin Bucetin
acetamidofluorene acetamidofluorene
Ticlopidine Ticlopidine
Tiopronin Tiopronin
Promethazine Promethazine
Sulpiride Sulpiride
Dantrolene Dantrolene
Clomipramine Clomipramine
Terbinafine Terbinafine
Lornoxicam Lornoxicam
Danazol Danazol
Etoposide Etoposide
N-Phenylanthranilic acid N-Phenylanthranilic acid
Ajmalin Ajmalin
Phenacetin Phenacetin
N-Nitrosodiethylamine N-Nitrosodiethylamine
Alpidem Alpidem
Venlafaxine Venlafaxine
Clozapine Clozapine
Buspirone Buspirone
Nefazodone Nefazodone
Triazolam Triazolam
Trimethadione Trimethadione
2-Bromoethylamine 2-Bromoethylamine
Doxorubicin Doxorubicin
Cyclosporin A Cyclosporin A
Cycloheximide Cycloheximide
Phorone Phorone
Bendazac Bendazac
Buthionine sulfoximine Buthionine sulfoximine
D-Galactosamine D-Galactosamine
Diethyl maleate Diethyl maleate
Rotenone Rotenone
N,N'-Diphenylmethylenediamine N,N'-Diphenylmethylenediamine
butylated hydroxyanisole butylated hydroxyanisole
Fungizone Fungizone
2,4-Dinitrophenol 2,4-Dinitrophenol
Fluoxetine hydrochloride Fluoxetine hydrochloride
Dexamethasone Dexamethasone
2-Nitrofluorene 2-Nitrofluorene
N-Methyl-N-nitrosourea N-Methyl-N-nitrosourea
Acetamide Acetamide
N-Nitrosomorpholine N-Nitrosomorpholine
treatmentid_abbr treatmentid_no
1-Naphthyl isothiocyanate ANIT 00009
Phenylbutazone PhB 00011
Rifampicin RIF 00008
Indomethacin IM 00015
Chlorpromazine CPZ 00016
Isoniazid INAH 00002
Acetaminophen APAP 00001
Clofibrate CFB 00006
Carbon tetrachloride CCL4 00003
Phenobarbital PB 00004
Methapyrilene MP 00025
Ethionine ET 00013
Carbamazepine CBZ 00018
Cimetidine CIM 00035
Fluphenazine FP 00037
Pirinixic acid WY 00030
Aspirin ASA 00014
Gemfibrozil GFZ 00031
Labetalol LBT 00040
Hexachlorobenzene HCB 00022
Amiodarone AM 00033
Allopurinol APL 00028
Benzbromarone BBr 00021
Nitrofurantoin NFT 00020
Diazepam DZP 00023
Griseofulvin GF 00043
Sulfasalazine SS 00034
Bromobenzene BBZ 00032
Cyclophosphamide CPA 00024
Omeprazole OPZ 00012
Allyl alcohol AA 00010
Valproic acid VPA 00005
Diclofenac DFNa 00019
Propylthiouracil PTU 00029
2H-1-Benzopyran-2-one CMA 00027
Haloperidol HPL 00036
Tetracycline TC 00048
Flutamide FT 00044
Glyburide GBC 00042
Azathioprine AZP 00046
Perhexiline PH 00045
Phenytoin PHE 00026
Doxepin Hydrochloride ADP 00039
Thioridazine TRZ 00038
Methyltestosterone MTS 00041
Lomustine LS 00049
Thioacetamide TAA 00017
Xolegel KC 00047
Ciprofloxacin CPX 00050
Pemoline PML 00051
Chlormezanone CMN 00052
Metformin MFM 00053
Tamoxifen TMX 00054
Ethinyl estradiol EE 00055
Methyldopa MDP 00056
Methimazole MTZ 00057
Monocrotaline MCT 00058
Retinol VA 00059
Quinidine QND 00074
Tacrine TAC 00060
Moxisylyte MXS 00061
Iproniazid IPA 00062
Chloramphenicol CMP 00064
Nitrofurazone NFZ 00065
Trimipramine IMI 00069
Amitriptyline AMT 00070
Hydroxyzine HYZ 00071
2-(4-Isobutylphenyl)propanoic acid IBU 00072
Naproxen NPX 00073
Furosemide FUR 00078
Fenofibrate FFB 00079
Chlorpropamide CPP 00080
Nicotinic acid NIC 00081
Erythromycin ethylsuccinate EME 00082
Ethambutol EBU 00083
Mefenamic acid MEF 00084
Pepcid FAM 00085
Ranitidine RAN 00086
Tannic acid TAN 00093
Captopril CAP 00094
Caffeine CAF 00097
Papaverine PAP 00098
Enalapril ENA 00095
Theophylline TEO 00096
Sulindac SUL 00100
D-Penicillamine PEN 00099
Disopyramide DIS 00102
Mexiletine MEX 00103
Acetazolamide ACZ 00108
Disulfiram DSF 00109
Colchicine COL 00113
Nifedipine NIF 00091
Diltiazem DIL 00092
Chlorpheniramine CHL 00090
Tolbutamide TLB 00114
Acarbose ACA 00116
Simvastatin SST 00117
Meloxicam MLX 00124
Chlormadinone CLM 00126
Benziodarone BZD 00130
Ethionamide ETH 00135
Nimesulide NIM 00136
Ethanol ETN 00137
Bucetin BCT 00139
acetamidofluorene AAF 00144
Ticlopidine TCP 00146
Tiopronin TIO 00104
Promethazine PMZ 00110
Sulpiride SLP 00115
Dantrolene DTL 00119
Clomipramine CPM 00121
Terbinafine TBF 00123
Lornoxicam LNX 00125
Danazol DNZ 00127
Etoposide ETP 00131
N-Phenylanthranilic acid NPAA 00140
Ajmalin AJM 00118
Phenacetin PCT 00138
N-Nitrosodiethylamine DEN 00145
Alpidem ADM 00171
Venlafaxine VLF 00172
Clozapine CZP 00174
Buspirone BPR 00173
Nefazodone NZD 00175
Triazolam TZM 00120
Trimethadione TMD 00122
2-Bromoethylamine BEA 00134
Doxorubicin DOX 00149
Cyclosporin A CSA 00142
Cycloheximide CHX 00A01
Phorone PHO 00A03
Bendazac BDZ 00129
Buthionine sulfoximine BSO 00A04
D-Galactosamine GaN 00A06
Diethyl maleate DEM 00A05
Rotenone ROT 00152
N,N'-Diphenylmethylenediamine DAPM 00155
butylated hydroxyanisole BHA 00156
Fungizone AMB 00157
2,4-Dinitrophenol DNP 00154
Fluoxetine hydrochloride FLX 00158
Dexamethasone DEX 00153
2-Nitrofluorene 2NF 00160
N-Methyl-N-nitrosourea MNU 00164
Acetamide AAA 00169
N-Nitrosomorpholine NMOR 00163
>
> treatmentInfo(TGGATESsmall) <- treatmentInfo(TGGATESsmall)
>
> treatmentNames(TGGATESsmall)
[1] "1-Naphthyl isothiocyanate" "Phenylbutazone"
[3] "Rifampicin" "Indomethacin"
[5] "Chlorpromazine" "Isoniazid"
[7] "Acetaminophen" "Clofibrate"
[9] "Carbon tetrachloride" "Phenobarbital"
[11] "Methapyrilene" "Ethionine"
[13] "Carbamazepine" "Cimetidine"
[15] "Fluphenazine" "Pirinixic acid"
[17] "Aspirin" "Gemfibrozil"
[19] "Labetalol" "Hexachlorobenzene"
[21] "Amiodarone" "Allopurinol"
[23] "Benzbromarone" "Nitrofurantoin"
[25] "Diazepam" "Griseofulvin"
[27] "Sulfasalazine" "Bromobenzene"
[29] "Cyclophosphamide" "Omeprazole"
[31] "Allyl alcohol" "Valproic acid"
[33] "Diclofenac" "Propylthiouracil"
[35] "2H-1-Benzopyran-2-one" "Haloperidol"
[37] "Tetracycline" "Flutamide"
[39] "Glyburide" "Azathioprine"
[41] "Perhexiline" "Phenytoin"
[43] "Doxepin Hydrochloride" "Thioridazine"
[45] "Methyltestosterone" "Lomustine"
[47] "Thioacetamide" "Xolegel"
[49] "Ciprofloxacin" "Pemoline"
[51] "Chlormezanone" "Metformin"
[53] "Tamoxifen" "Ethinyl estradiol"
[55] "Methyldopa" "Methimazole"
[57] "Monocrotaline" "Retinol"
[59] "Quinidine" "Tacrine"
[61] "Moxisylyte" "Iproniazid"
[63] "Chloramphenicol" "Nitrofurazone"
[65] "Trimipramine" "Amitriptyline"
[67] "Hydroxyzine" "2-(4-Isobutylphenyl)propanoic acid"
[69] "Naproxen" "Furosemide"
[71] "Fenofibrate" "Chlorpropamide"
[73] "Nicotinic acid" "Erythromycin ethylsuccinate"
[75] "Ethambutol" "Mefenamic acid"
[77] "Pepcid" "Ranitidine"
[79] "Tannic acid" "Captopril"
[81] "Caffeine" "Papaverine"
[83] "Enalapril" "Theophylline"
[85] "Sulindac" "D-Penicillamine"
[87] "Disopyramide" "Mexiletine"
[89] "Acetazolamide" "Disulfiram"
[91] "Colchicine" "Nifedipine"
[93] "Diltiazem" "Chlorpheniramine"
[95] "Tolbutamide" "Acarbose"
[97] "Simvastatin" "Meloxicam"
[99] "Chlormadinone" "Benziodarone"
[101] "Ethionamide" "Nimesulide"
[103] "Ethanol" "Bucetin"
[105] "acetamidofluorene" "Ticlopidine"
[107] "Tiopronin" "Promethazine"
[109] "Sulpiride" "Dantrolene"
[111] "Clomipramine" "Terbinafine"
[113] "Lornoxicam" "Danazol"
[115] "Etoposide" "N-Phenylanthranilic acid"
[117] "Ajmalin" "Phenacetin"
[119] "N-Nitrosodiethylamine" "Alpidem"
[121] "Venlafaxine" "Clozapine"
[123] "Buspirone" "Nefazodone"
[125] "Triazolam" "Trimethadione"
[127] "2-Bromoethylamine" "Doxorubicin"
[129] "Cyclosporin A" "Cycloheximide"
[131] "Phorone" "Bendazac"
[133] "Buthionine sulfoximine" "D-Galactosamine"
[135] "Diethyl maleate" "Rotenone"
[137] "N,N'-Diphenylmethylenediamine" "butylated hydroxyanisole"
[139] "Fungizone" "2,4-Dinitrophenol"
[141] "Fluoxetine hydrochloride" "Dexamethasone"
[143] "2-Nitrofluorene" "N-Methyl-N-nitrosourea"
[145] "Acetamide" "N-Nitrosomorpholine"
>
> treatmentNames(TGGATESsmall) <- treatmentNames(TGGATESsmall)
>
>
> ## @annotation
>
> annotation(TGGATESsmall)
$name
[1] "TGGATES Human LDH"
$dateCreated
[1] "Tue Mar 10 13:19:27 2020"
$sessionInfo
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylibError in grepl(LAver, lapack, fixed = TRUE) : invalid 'pattern' argument
Calls: <Anonymous> -> print.sessionInfo -> grepl
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘toxicoGxCaseStudies.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/ToxicoGx.Rcheck/00check.log’
for details.
ToxicoGx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ToxicoGx ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘ToxicoGx’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (ToxicoGx)
ToxicoGx.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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> library(testthat)
> library(ToxicoGx)
Loading required package: CoreGx
Loading required package: BiocGenerics
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'ToxicoGx'
The following objects are masked from 'package:CoreGx':
showSigAnnot, subsetTo, summarizeMolecularProfiles,
summarizeSensitivityProfiles
> test_check("ToxicoGx")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 53 ]
>
> proc.time()
user system elapsed
15.928 0.503 16.587
ToxicoGx.Rcheck/ToxicoGx-Ex.timings
| name | user | system | elapsed |