CRAN Package Check Results for Package HAP.ROR

Last updated on 2020-04-09 09:48:12 CEST.

Check Details

Version: 1.0
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to 'ape' which was already attached by Depends.
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     'ape' 'hash'
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0
Check: R code for possible problems
Result: NOTE
    AIC: no visible global function definition for 'hash'
    AIC: no visible global function definition for 'values'
    AIC: no visible global function definition for 'contr.treatment'
    AIC: no visible global function definition for 'values<-'
    AIC: no visible global function definition for 'glm'
    AIC: no visible binding for global variable 'binomial'
    AIC: no visible global function definition for 'fitted'
    ODS.ror: no visible global function definition for 'write.table'
    ODS.ror: no visible global function definition for 'hash'
    ODS.ror: no visible global function definition for 'values<-'
    ODS.ror: no visible global function definition for 'keys'
    ODS.ror: no visible global function definition for 'values'
    ODS.ror: no visible global function definition for 'read.tree'
    ODS.ror: no visible global function definition for 'colorRampPalette'
    ODS.ror: no visible global function definition for 'nodelabels'
    cc.sim: no visible global function definition for 'hash'
    cc.sim: no visible global function definition for 'values<-'
    cc.sim: no visible global function definition for 'values'
    cc.sim: no visible global function definition for 'rbinom'
    collapse: no visible global function definition for 'hash'
    collapse: no visible global function definition for 'values<-'
    collapse: no visible global function definition for 'keys'
    collapse: no visible global function definition for 'values'
    deletion: no visible global function definition for 'hash'
    deletion: no visible global function definition for 'values<-'
    deletion: no visible global function definition for 'keys'
    deletion: no visible global function definition for 'values'
    deletion: no visible global function definition for 'pchisq'
    grp.list: no visible global function definition for 'hash'
    grp.list: no visible global function definition for 'values'
    Undefined global functions or variables:
     binomial colorRampPalette contr.treatment fitted glm hash keys
     nodelabels pchisq rbinom read.tree values values<- write.table
    Consider adding
     importFrom("grDevices", "colorRampPalette")
     importFrom("stats", "binomial", "contr.treatment", "fitted", "glm",
     "pchisq", "rbinom")
     importFrom("utils", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-osx-x86_64, r-patched-solaris-x86

Version: 1.0
Check: Rd line widths
Result: NOTE
    Rd file 'HAP.ROR-package.Rd':
     \examples lines wider than 100 characters:
     ODS.ror(case.sub=case.sub, ctl.sub=ctl.sub, lib.sub=lib.sub, lib.sub.names=lib.sub.names, records=ror.res$records, dev.list=ror.res$dev ... [TRUNCATED]
    
    Rd file 'HAP.ror.Rd':
     \usage lines wider than 90 characters:
     HAP.ror(case.sub, ctl.sub, lib.sub, lib.sub.names, alpha = 0.01, ref.level = NA, display.proc = TRUE)
    
    Rd file 'ODS.ror.Rd':
     \usage lines wider than 90 characters:
     ODS.ror(case.sub, ctl.sub, lib.sub, lib.sub.names, records, dev.list, AIC.list, deleted.snps.ls, proteinf, locus = "DRB1*", ref.level = ... [TRUNCATED]
     \examples lines wider than 100 characters:
     ODS.ror(case.sub=case.sub, ctl.sub=ctl.sub, lib.sub=lib.sub, lib.sub.names=lib.sub.names, records=ror.res$records, dev.list=ror.res$dev ... [TRUNCATED]
    
    Rd file 'cc.sim.Rd':
     \usage lines wider than 90 characters:
     cc.sim(n.ctrl, n.case, beta0, beta1, case.sub, ctl.sub, lib.sub, lib.sub.names, risk.type = "AA", risk.inx = 2, risk.names = c("301", " ... [TRUNCATED]
    
    Rd file 'deletion.Rd':
     \usage lines wider than 90 characters:
     deletion(lib, lib.names, case.sub, ctl.sub, aic.now, dev.now, df.now, rank = FALSE, cut = -1, delete.snp = -1, ref = "NA", alpha = 0.05 ... [TRUNCATED]
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0
Check: examples
Result: ERROR
    Running examples in 'HAP.ROR-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: HAP.ROR-package
    > ### Title: Recursive Organizer (ROR)
    > ### Aliases: HAP.ROR-package HAP.ROR
    >
    > ### ** Examples
    >
    > library("HAP.ROR")
    > data(case.sub)
    > data(ctl.sub)
    > data(lib.sub)
    > data(lib.sub.names)
    > ror.res <- HAP.ror(case.sub, ctl.sub, lib.sub, lib.sub.names, alpha=0.01, ref.level="101");
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92 1 2 4 7 13 14 15 16 39 83 85 86 89 90
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92 1 2 4 7 13 14 15 16 39 83 85 86 89 90 9 10 11 20 30 31 32 33 34 36 43 64 91
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92 1 2 4 7 13 14 15 16 39 83 85 86 89 90 9 10 11 20 30 31 32 33 34 36 43 64 91 8 58 74 75 87 88
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92 1 2 4 7 13 14 15 16 39 83 85 86 89 90 9 10 11 20 30 31 32 33 34 36 43 64 91 8 58 74 75 87 88 3 5 21 27 28 44 45 46 82 84
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92 1 2 4 7 13 14 15 16 39 83 85 86 89 90 9 10 11 20 30 31 32 33 34 36 43 64 91 8 58 74 75 87 88 3 5 21 27 28 44 45 46 82 84 6 19 38 73
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    >
    > # grouping result:
    > round(ror.res$dev.list, 2);
    [1] 0.00 0.02 4.29 3.51 3.75 0.21 4.90 3.32 -91.25
    > round(ror.res$AIC.list, 2);
    [1] 0.95 0.88 0.04 0.06 0.05 0.65 0.03 0.07 0.00
    > ror.res$df.list;
    [1] 1 1 1 1 1 1 1 1 -75
    > ror.res$deleted.snps;
     [1] 1 2 3 4 5 7 8 9 10 11 12 13 14 15 16 17 18 20 21 22 23 24 25 26 27
    [26] 28 29 30 31 32 33 34 35 36 37 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53
    [51] 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 74 75 76 77 78 79
    [76] 80 81 82 83 84 85 86 87 88 89 90 91 92
    > ror.res$grp.result;
     grp
     [1,] "DRB1*01:01" "1"
     [2,] "DRB1*03:01" "1"
     [3,] "DRB1*04:01" "1"
     [4,] "DRB1*04:04" "1"
     [5,] "DRB1*07:01" "1"
     [6,] "DRB1*08:01" "1"
     [7,] "DRB1*09:01" "1"
     [8,] "DRB1*13:01" "1"
     [9,] "DRB1*13:02" "1"
    > ror.res$significant;
    [1] 1
    > # model summary:
    > ror.res$model.summary;
    
    Call:
    glm(formula = grp.sample[, 1] ~ allele.factor, family = binomial)
    
    Deviance Residuals:
     Min 1Q Median 3Q Max
    -1.435 -1.435 0.940 0.940 0.940
    
    Coefficients:
     Estimate Std. Error z value Pr(>|z|)
    (Intercept) 0.5878 0.2494 2.356 0.0185 *
    allele.factor -18.2099 1819.5131 -0.010 0.9920
    ---
    Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
     Null deviance: 104.539 on 76 degrees of freedom
    Residual deviance: 91.246 on 75 degrees of freedom
    AIC: 95.246
    
    Number of Fisher Scoring iterations: 17
    
    > # output tables and figures used for ror result
    > data(proteinf)
    > ODS.ror(case.sub=case.sub, ctl.sub=ctl.sub, lib.sub=lib.sub, lib.sub.names=lib.sub.names, records=ror.res$records, dev.list=ror.res$dev.list, AIC.list=ror.res$AIC.list, deleted.snps.ls=ror.res$deleted.snps.ls, proteinf=proteinf, locus="DRB1*", ref.level="101");
    Error in if (sv3[i] < survived[j, 5]) { :
     missing value where TRUE/FALSE needed
    Calls: ODS.ror
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 1.0
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     'ROR.sv'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86

Version: 1.0
Check: examples
Result: ERROR
    Running examples in ‘HAP.ROR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: HAP.ROR-package
    > ### Title: Recursive Organizer (ROR)
    > ### Aliases: HAP.ROR-package HAP.ROR
    >
    > ### ** Examples
    >
    > library("HAP.ROR")
    > data(case.sub)
    > data(ctl.sub)
    > data(lib.sub)
    > data(lib.sub.names)
    > ror.res <- HAP.ror(case.sub, ctl.sub, lib.sub, lib.sub.names, alpha=0.01, ref.level="101");
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92 1 2 4 7 13 14 15 16 39 83 85 86 89 90
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92 1 2 4 7 13 14 15 16 39 83 85 86 89 90 9 10 11 20 30 31 32 33 34 36 43 64 91
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92 1 2 4 7 13 14 15 16 39 83 85 86 89 90 9 10 11 20 30 31 32 33 34 36 43 64 91 8 58 74 75 87 88
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92 1 2 4 7 13 14 15 16 39 83 85 86 89 90 9 10 11 20 30 31 32 33 34 36 43 64 91 8 58 74 75 87 88 3 5 21 27 28 44 45 46 82 84
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    deleting: 49 50 51 61 68 70 76 78 80 81 26 40 41 48 55 56 60 67 77 79 12 23 25 29 52 57 59 62 63 65 66 69 71 72 17 18 22 24 35 37 42 47 53 54 92 1 2 4 7 13 14 15 16 39 83 85 86 89 90 9 10 11 20 30 31 32 33 34 36 43 64 91 8 58 74 75 87 88 3 5 21 27 28 44 45 46 82 84 6 19 38 73
    Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
    >
    > # grouping result:
    > round(ror.res$dev.list, 2);
    [1] 0.00 0.02 4.29 3.51 3.75 0.21 4.90 3.32 -91.25
    > round(ror.res$AIC.list, 2);
    [1] 0.95 0.88 0.04 0.06 0.05 0.65 0.03 0.07 0.00
    > ror.res$df.list;
    [1] 1 1 1 1 1 1 1 1 -75
    > ror.res$deleted.snps;
     [1] 1 2 3 4 5 7 8 9 10 11 12 13 14 15 16 17 18 20 21 22 23 24 25 26 27
    [26] 28 29 30 31 32 33 34 35 36 37 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53
    [51] 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 74 75 76 77 78 79
    [76] 80 81 82 83 84 85 86 87 88 89 90 91 92
    > ror.res$grp.result;
     grp
     [1,] "DRB1*01:01" "1"
     [2,] "DRB1*03:01" "1"
     [3,] "DRB1*04:01" "1"
     [4,] "DRB1*04:04" "1"
     [5,] "DRB1*07:01" "1"
     [6,] "DRB1*08:01" "1"
     [7,] "DRB1*09:01" "1"
     [8,] "DRB1*13:01" "1"
     [9,] "DRB1*13:02" "1"
    > ror.res$significant;
    [1] 1
    > # model summary:
    > ror.res$model.summary;
    
    Call:
    glm(formula = grp.sample[, 1] ~ allele.factor, family = binomial)
    
    Deviance Residuals:
     Min 1Q Median 3Q Max
    -1.435 -1.435 0.940 0.940 0.940
    
    Coefficients:
     Estimate Std. Error z value Pr(>|z|)
    (Intercept) 0.5878 0.2494 2.356 0.0185 *
    allele.factor -18.2099 1819.5131 -0.010 0.9920
    ---
    Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
     Null deviance: 104.539 on 76 degrees of freedom
    Residual deviance: 91.246 on 75 degrees of freedom
    AIC: 95.246
    
    Number of Fisher Scoring iterations: 17
    
    > # output tables and figures used for ror result
    > data(proteinf)
    > ODS.ror(case.sub=case.sub, ctl.sub=ctl.sub, lib.sub=lib.sub, lib.sub.names=lib.sub.names, records=ror.res$records, dev.list=ror.res$dev.list, AIC.list=ror.res$AIC.list, deleted.snps.ls=ror.res$deleted.snps.ls, proteinf=proteinf, locus="DRB1*", ref.level="101");
    Error in if (sv3[i] < survived[j, 5]) { :
     missing value where TRUE/FALSE needed
    Calls: ODS.ror
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-osx-x86_64, r-patched-solaris-x86

Version: 1.0
Check: R code for possible problems
Result: NOTE
    AIC: no visible global function definition for ‘hash’
    AIC: no visible global function definition for ‘values’
    AIC: no visible global function definition for ‘contr.treatment’
    AIC: no visible global function definition for ‘values<-’
    AIC: no visible global function definition for ‘glm’
    AIC: no visible binding for global variable ‘binomial’
    AIC: no visible global function definition for ‘fitted’
    ODS.ror: no visible global function definition for ‘write.table’
    ODS.ror: no visible global function definition for ‘hash’
    ODS.ror: no visible global function definition for ‘values<-’
    ODS.ror: no visible global function definition for ‘keys’
    ODS.ror: no visible global function definition for ‘values’
    ODS.ror: no visible global function definition for ‘read.tree’
    ODS.ror: no visible global function definition for ‘colorRampPalette’
    ODS.ror: no visible global function definition for ‘plot’
    ODS.ror: no visible global function definition for ‘nodelabels’
    cc.sim: no visible global function definition for ‘hash’
    cc.sim: no visible global function definition for ‘values<-’
    cc.sim: no visible global function definition for ‘values’
    cc.sim: no visible global function definition for ‘rbinom’
    collapse: no visible global function definition for ‘hash’
    collapse: no visible global function definition for ‘values<-’
    collapse: no visible global function definition for ‘keys’
    collapse: no visible global function definition for ‘values’
    deletion: no visible global function definition for ‘hash’
    deletion: no visible global function definition for ‘values<-’
    deletion: no visible global function definition for ‘keys’
    deletion: no visible global function definition for ‘values’
    deletion: no visible global function definition for ‘pchisq’
    grp.list: no visible global function definition for ‘hash’
    grp.list: no visible global function definition for ‘values’
    Undefined global functions or variables:
     binomial colorRampPalette contr.treatment fitted glm hash keys
     nodelabels pchisq plot rbinom read.tree values values<- write.table
    Consider adding
     importFrom("grDevices", "colorRampPalette")
     importFrom("graphics", "plot")
     importFrom("stats", "binomial", "contr.treatment", "fitted", "glm",
     "pchisq", "rbinom")
     importFrom("utils", "write.table")
    to your NAMESPACE file.
Flavors: r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64